The duo went clear with just over a kilometre to go on the final lap of the 63km event, powering away from their breakaway companions Marc Hirschi (UAE-Team Emirates) and Geoffrey Bouchard (AG2R Citroën).
In the end it was a comfortable sprint win for three-time world champion Sagan - wearing the ciclamino jersey he had as points classification winner at the Giro - against the much lighter Bernal, who was wearing the famous maglia rosa.
Hirschi won the sprint for third several seconds ahead of the rest of the bunch.
The decisive selection happened with two laps and just over 4km to go, as Bernal attacked, and was followed by Bouchard, Hirschi and finally Sagan, leaving the main bunch behind to fight for fifth place.
The Giro d’Italia Criterium Dubai consisted of a 30-lap exhibition race held on a 2.1-kilometre circuit, the course forming the shape of the Giro d’Italia’s ‘Amore Infinito’ symbol used to inspire the trophy of the Italian Grand Tour.
According to race organisers RCS, it is believed to be the first ever sporting event to take place at a World Expo.
Speaking after his victory, Sagan said: "I’m very happy that I could be here, and this is a special race for all of us from the Giro d’Italia. I think we had the best riders from this year’s Giro. This short criterium is a special thing.
"It’s nice for the fans. This criterium is special because this is the Expo in Dubai and all the world is here. I’m very happy with this win, a victory is much better than not. I just appreciated that I could be here. I have to say thanks to my teammates because they controlled the race for me and did a really good job."
Sagan continued: "From the start I tried to be in the front, also for the points classification. After two sprints I saw Elia [Viviani] was much better and so I tried a different tactic. It was really fast, and definitely someone was going to go in the last three laps, and I had to recover and wait for the last two laps.
"I just decided I was going to stay on the wheel and see what was going to happen. It just happened so fast that three guys attacked, and I went at the last moment. I almost missed it, and in the end was good."
The winner of the points classification was Elia Viviani (Cofidis), the most combative was judged to have been Attila Valter (Groupama-FDJ), and Filippo Ganna (Ineos Grenadiers) won the fastest lap prize.
Yousif Mirza (UAE-Team Emirates), Valter and Juraj Sagan (Bora-Hansgrohe) were part of an early break, that at one point had ten seconds on the bunch, but they were soon caught thanks to the efforts of the three Ineos Grenadiers riders.
In its place, an eight man move that included Fabio Aru (Qhubeka-NextHash), Brandon Rivera (Ineos Grenadiers), Lorenzo Fortunato (Eolo-Kometa) and Viviani also went clear, by up to nine seconds. Again, they were caught.
Ganna suffered mechanical problems late on in the race, but then attacked solo with seven laps to go; he was eventually reeled in by a chasing group that consisted of Anass Aït El Abdia (Bahrain Cycling Academy) and Valter. That group was caught with two laps to go.
In their place came the winning move of Bernal, Bouchard, Hirschi and Sagan.
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