Hughes finished the feature race yesterday in eighth place giving him pole position for the sprint race today.
Antonio Fuoco, winner of the main race, retired on the final lap. Nyck de Vries finished the race in eighth.
At the start it was a collision instantly which took out both Artur Janosz and Ralph Boschung. The crash meant a virtual safety car.
Hughes had lost the lead at the start due to a slow start, being passed by Arjun Maini. Just before the VSC period, Hughes retook the lead although he was under investigation at the time for whether he had made the move before or during the VSC period.
When the race was resumed, Hughes continued to lead and took the win with a 2.6 second lead over fellow Brit Jack Aitken.
Jake Dennis, Matt Parry and Nyck de Vries rounded out the points scorers
Bahrain International Circuit - Winter testing