Bagnaia wins first ever MotoGP sprint at Portuguese Grand Prix
Introduced this season in a bid to make the sport more entertaining, sprints will be run a day before the race and are approximately 50% of the full distance, which was 12 laps around the Portimao circuit.
Marc Marquez stunned the field when he took pole position in qualifying earlier with the help of a slipstream, but his Honda was no match for the Ducatis whose straight-line speed helped Bagnaia take the lead in the opening lap.
Marquez struggled to keep his rivals at bay and soon Pramac Racing's Jorge Martin went past him and even took the lead from Bagnaia while Jack Miller and Miguel Oliveira also overtook the six-times champion who dropped to fifth.
But with two laps to go, Marquez saw an opening when Oliveira and Miller jostled for position, performing a risky double overtake to move up and finish third.
On the final lap, Martin looked set to take the chequered flag but the Spaniard went wide on a turn, opening the door for Bagnaia to storm ahead and win the sprint.
"It was fun, but it was difficult for the win," said Bagnaia, who had dropped to third midway through the sprint.
"I had fun, I enjoyed it a lot. I took my time in the first part of the race and then in the last (stages) I just tried to push. Jorge had better traction but had more problems than me with the front (tyre)."
Bagnaia's teammate Enea Bastianini, who had stormed from sixth to second on the opening lap and looked set for a points finish, was taken out by Luca Marini in an overtake gone wrong.
The Italian Ducati rider was later taken to hospital after sustaining a right scapula fracture in the crash and his team said he would have to sit out Sunday's race as well as the Argentine Grand Prix next weekend.
Bastianini is the second rider who will miss the race after GasGas Factory Racing Tech3's Pol Espargaro was ruled out with multiple injuries following a horrific crash in Friday's practice.
Former champions Fabio Quartararo and Honda's Joan Mir were involved in a collision which saw the latter crash while the Yamaha rider managed to keep his balance, but he lost several positions as a result, eventually finishing 10th.
But he lost several positions as a result, eventually finishing 10th which gave him no points. Unlike Sunday's races, only the first nine riders can claim points in the sprint.
Sunday's race will have the same grid order after the qualifying session with Marquez on pole.