It was the second victory for Nibali in his home Monument after a similarly-executed win on the same run-in to Como in 2015.
"I got big support from my team I had great physical condition from the end of the season, but everyone was looking to me as the favourite so it wasn't easy to win," Nibali said.
"Today my plan was just to have a great race. I've had a lot of good placings this year but without the big win that I was looking for and to win a Monument it is always something great."
Nibali moved into a lead group with 18km to go on the Civiglio, the penultimate climb of the day. He then bridged across to attacker Thibaut Pinot (FDJ) making a formidable two-man escape that quickly distanced the others.
The Frenchman has largely overcome his descending fears over the past few seasons, but was no match for Nibali on the technical, narrow descent of the Civiglio.
Although Pinot managed to keep Nibali to a handful of seconds at the foot of the final climb of the San Fermo della Battaglia, he lost ground on the climb and the subsequent descent.
Ahead, Nibali swept down the narrow, sinuous descent, bunny-hopping speed humps and railing the corners to build up an unassailable lead.
Alaphilippe, another notable descender, shot out of the chasing group and went off in pursuit of Nibali in the final kilometers, but ran out of time to close the gap. He held on for second ahead of a chasing group led home by Moscon.
"It's incredible," Alaphilippe said. "I didn't expect to finish on the podium today. I had a strange feeling after the World Championships, but I kept focused and my team did a really good job. I did my best but I couldn't follow Nibali when he attacked. I'm not disappointed, it's already something special to finish on the podium of a Monument."
The Frenchman took a moment to mention his teammate Laurens De Plus, who suffered a horrific crash on the descent of the Sormano in which he flew over the guardrail into a ravine.
"My thoughts also go to my teammate who crashed during the race while he was at the front. I heard he's OK, I strongly hope so. I want to thank my team for their work in my favour today, and I will return to the Italian monuments with the aim of doing even better than third in Milan-San Remo and second at Il Lombardia."
Moscon, who attacked just before Pinot sparked the winning move, was satisfied with a podium finish to close out an exceptional second professional year.
"Even if I didn't win a race this year, a podium here in Como is fantastic and worth a victory – it's the best way to close my season," Moscon said. "Nibali was the strongest on the last climb. I tried to attack Civiglio but everybody was tired after 200km or more of racing pretty hard. After the Sormano wall, your legs feel stiff. Even if I went with Nibali I'd have been dropped in the next climb like Pinot was. I'm happy with third place."
How it unfolded
Sunshine and blue skies greeted the riders as they set off from Bergamo. Right from the start, Davide Ballerini (Androni Sidermec) and Jacques Janse Van Rensburg (Dimension Data) jumped and took a short lead. They were soon joined by Lorenzo Rota (Bardiani CSF), Matthias Le Turnier (Cofidis), Pier Paolo De Negri (Nippo Vini Fantini) and Lennard Hofstede (Sunweb) to create the first breakaway.
The group built up a gap of 12 minutes, which seemed to put a scare on the peloton. Bahrain-Merida, looking to put Vincenzo Nibali atop the podium, and Cannondale-Drapac, riding for Rigoberto Uran, led the chase. The gap continued to drop as the climbing started and with 100km to go, the break had only six minutes, and Movistar had joined in the chase work.
Then the action finally started. Trek-Segafredo, Lotto-Soudal and Team Sky hit the front of the field and pushed the pace. With 73km to go, the gap had fallen to two minutes and within two kilometers was nearing the one minute mark.
A chase group soon formed ahead of the peloton: Jesus Herrada (Movistar) was the first to go, and he was then joined by Andriy Grivko (Astana), Primoz Roglic (LottoNL-Jumbo), Laurens De Plus (Quick-Step Floors), Jan Polanc (UAE Team Emirates), Rodolfo Torres (Androni Sidermac), Mikael Cherel (AG2R La Mondiale) and Alessandro De Marchi (BMC). Herrada was soon dropped.
That group charged along as the lead group started falling apart. Soon only Ballerini and Le Turnier were in front ahead of the new group, which had also dropped some riders and picked up some of the drop-outs from the lead group, in a rapidly-changing situation.
The first major climb of the day was the famed Madonna del Ghisallo, and as the two leaders neared the top, Le Turnier attacked, leaving Ballerini behind, with Cherel and De Plus chasing not far behind. They caught and passed the Frenchman before the summit, but he joined them again on the descent.
The trio slowly built up 30 to 40 seconds on chasers Roglic, Ballerini, De Negri, Hofstede, Rota, Janse van Rensburg, Valerio Conti (UAE Team Emirates) and Winner Anacona (Movistar). This group too started dropping riders, and soon was only 30 seconds ahead of the field. They started up the day's biggest climb, the Sormano. The leading trio had 38 seconds on the chase group with the field at 0:49. Cherel proved to be the strongest and slowly moved away from the other two on the narrow road up.
De Plus continued to give chase, but Le Turnier ended up back with Roglic and a UAE rider, and they too were caught by a large chasing group. Cherel hit the summit about 30 seconds ahead of De Plus, with the field to about another 30 seconds. The long and relatively dangerous descent led to a flattish section on the way to the penultimate climb.
The dangerous descent proved itself in a horrifying crash with just over 40km to go. De Plus overcooked a turn, hit the guardrail and was launched up over the barrier, his bike flying into the nearby trees. Many feared the worst, but the team reported that he was not seriously injured. The gap back to the field grew after that, going over a minute. Eventually Philippe Gilbert (Quick-Step Floors) and De Marchi attacked, moving up to within 30 seconds of Cherel. Pello Bilbao (Astana) was able to work his way up to the duo, only 15 seconds behind Cherel with 30 km left.
The trio finally caught the leader with 24km to go. They took 30 seconds with them as they headed up the next climb, the Civiglio, with gradients up to 10 percent. Cherel had to drop back and was picked up by the field, then only 14 seconds back at 20km. With 18 km to go, the last of the three leaders was absorbed back into the field. Gianni Moscon (Sky) took off, followed by Sam Oomen (Sunweb). Others gave chase, including Thibaut Pinot (FDJ) and Vincenzo Nibali (Bahrain Merida).
Pinot caught and passed the leaders, and held a small gap over them before Nibali joined the Frenchman. The two flew down the short descent, with Nibali maintaining a lead. The Italian put his experience and fearlessness to good use to extend his advantage.
Rigoberto Uran (Cannondale-Drapac) also gave chase and was joined by Moscon, but with 8 km, they were still 45 seconds behind.
There was one more climb to go and Nibali started up it with 17 seconds in hand. Uran and Moscon were caught again and other attacks followed, including Diego Rosa (Sky), Domenico Pozzovivo (AG2R), Nairo Quintana (Movistar) and Fabio Aru (Astana).
Nibali kept his calm and built up his lead, topping the last climb with 38 seconds on Pinot and 45 seconds on the field. Julian Alaphilippe (Quick-Step) caught Pinot, but the other chasers were only seconds behind. Alaphilippe then took off alone in search of second place.
The experienced Italian held on to his lead and had plenty of time to celebrate on the final hundred meters before crossing the finish line for his second Lombardia title and 50th pro win. Alaphilippe came through alone 28 seconds later, and Moscon won the sprint of the chase group to claim third place ten seconds later.
