The Briton set a lap time of 1:14.563, running as the second driver in the final stage of qualifying. However, the four drivers that set times after him couldn't better his time, allowing the BMW driver to take his second career pole.
Mercedes was the only team to get both of its cars into Super Pole, with Vandoorne securing a front row start for the German squad.
His teammate Nyck de Vries was third, and looked to be challenging Sims for pole before he lost half a second in the final sector.
Despite being part of the second qualifying group, Sam Bird's lap time was enough to see him through to Super Pole - although on his last lap, he made a mistake early on, which put him out of contention.
The Envision Virgin racer placed himself into fifth place ahead of Jerome D'Ambrosio, who was the slowest of the Super Pole drivers.
Porsche's debut qualifying session in Formula E saw it just miss out on Super Pole, as Andre Lotterer, who has made the switch from Techeetah for the season, just missed the cut in his group.
Reigning champion Jean-Eric Vergne was part of the first qualifying group, and therefore suffered with a slippery track.
In group three, Nico Mueller and James Calado both hit the wall at the same point just moments apart - putting both of them out of the session.
Brendon Hartley's session was a difficult one due to the lack of running that he had during the opening two practice sessions. The Kiwi could only manage the 18th fastest time.
Bahrain International Circuit - Winter testing