The Comtec driver, who started the race down in 14th, made his way up to seventh by the end of the first lap as the first spots of rain started to fall.
He was one of several drivers to brave the first shower without coming in for wets, and when the rain stopped many of the frontrunners came in for their mandatory pitstop for fresh slick tyres.
But Yelloly and Marco Sorensen stayed out longer than most, with the Dane leading. However, when Lotus driver Sorensen finally came in, the rain started to fall again.
That enabled Yelloly to make his only stop of the race and switch to wets, while Sorensen had to come in again to get himself on the correct tyre.
While Yelloly enjoyed a lead of almost half a minute, Sorensen had to fight with Andre Negrao (Draco), who had also managed to stay out until the second shower and make only one stop. But the Brazilian was struggling for pace, partly due to a damaged front wing.
Sorensen eventually made it through three laps from the end with a daring pass around the outside of Turn 5. That left Negrao to defend from the ISR duo of Jake Rosenzweig and Sam Bird.
He managed to hang on to his podium place, but Rosenzweig went off just a few corners from the flag, promoting Bird to fourth.
Bird's championship rival Robin Frijns was just behind, after the pair had fought wheel to wheel for the lead early in the race. Bird came out on top in that duel, but lost out to the Dutchman during their first stops. He put that right when they came back in for wets, staying out a lap longer and jumping the Fortec driver again.
Of the drivers to gamble on the early switch to wets, which meant making three stops in total as they reacted to each change in conditions, P1's Daniil Move and Carlin's Kevin Magnussen came home highest in seventh and eighth.
Race one winner Jules Bianchi (Tech 1) was in the thick of the battle for the lead in the early laps, and was the first car to pit for new slicks when it was clear the first rainshower wasn't going to last. However, the Ferrari junior driver went off on his out-lap, and spent the rest of the race running almost a lap down.