His late attack only earned him a slim two-second advantage, but it was a significant psychological blow. It was Nibali's first victory at the Tour de France and he knew it also gave him a place in the history of cycling's Grand Tours.
"I'm very happy, this is a special, unexpected moment of happiness," he said with a smile in his press conference and in the mixed zone after pulling on the yellow jersey.
"I knew I had the form to win, and taking the yellow jersey means I've now worn all three Grand Tour leader's jerseys after wearing the red jersey at the Vuelta a Espana and the pink jersey at the Giro d'Italia. I think only Alberto Contador has done that in modern cycling." (ed. Cadel Evans and Bradley Wiggins have also worn all three jerseys.)
Nibali received scant attention from the Tour de France media before the race, with only a handful of journalists attending his press conference, while hundreds listened to Froome and Contador. Many people think that the 2014 Tour de France is a two-horse race. Nibali reminded them it he is also a threat and that attacks could come at any time.
"It didn't bother me what the media said, I always believed in my chances," he said.
"I came to do my very best at the Tour de France, and I think I've showed that with this win. Obviously the Tour de France does not finished here, the road ahead is long but I'm confident I can do well."
Nibali's victory also put an end to any tension within his Astana team. Today is the 16th anniversary of the creation of the Kazakhstan capital Astana and also the birthday of the country's president Nursultan Nazarbayev.
"The team always believed in me and this win showed that we've worked well. It's an important win for Kazakhstan and in the capital Astana. It's a day for them to celebrate too," Nibali said.
"I'm also thinking about what is happening in my family's home town [in Messina, in Sicily]. I'm sure they're over the moon at home and I can't wait to speak to them. This yellow jersey is for them."
The right moment
Nibali explained that he made his attack at the right moment. There was a strong headwind in the valley road outside of Sheffield but with teammate Jakob Fuglsang blocking behind and former teammate and friend Peter Sagan refusing to chase, he gained enough of a gap to win alone.
"In the finale lots of riders all tried things because we were scared of a big attack," he said.
"Alberto (Contador) was up there and set the pace. Froome was controlling things and almost seemed to attack. The first real move was made by Fuglsang. Sagan closed him down and then at 1.5km to go, I found the right moment and space to go for it."
"We were lined out and Sagan had just chased Fuglsang, there was a ease in the speed and so it was good form me. It's never easy to attack like that, there was a lot of head wind, which scared me but I made it."
Nibali dominated the 2013 Giro d'Italia but has struggled to re-find the same form. However he is confident he is back to his best for the Tour de France.
"It's a year later, so it's difficult to compare my form to the Giro d'Italia but the training has been the same and so my form is good; I think about same as the Giro," he said.
"We'll see day by day there's a lot of hard stages to come and there are some big rivals to face like Froome and Contador."