Sprint winner Espargaro was second for much of the race, but the Spaniard took advantage of Vinales' worn-out front tyre to surge into the lead with four laps left and seal the win at the Circuit de Barcelona-Catalunya - located seven kilometres from his home town of Granollers.
Espargaro dedicated his victory to world champion Bagnaia, whose leg was run over by KTM's Brad Binder straight after the crash. Bagnaia was conscious and taken to hospital for treatment.
"First thing I want to say is they told me what happened to Pecco (Bagnaia) is nothing serious, that's lucky. This win is for him," Espargaro said.
The win erased the memories of Espargaro's premature celebration at last year's Catalunya GP, when he was one lap away from sealing second position but thought the race was over and began waving to his fans.
"I made a mistake when I was trying to overtake Maverick and I lost a lot of ground. I thought for a moment 'you will not catch him, he's very fast'. But I went to the limit for 25 minutes and I made it happen," Espargaro said.
Aprilia had looked on course for a clean sweep, but Pramac Racing riders Jorge Martin and Johann Zarco leapfrogged Miguel Oliveira (RNF Aprilia) to finish third and fourth.
After a chaotic start, the race was restarted for 23 laps and Martin rocketed off the line to take the lead heading into turn one, but he was quickly overtaken by Vinales and Espargaro - who recorded Aprilia's first-ever one-two in the competition.
"First and second for Aprilia, that's a historic result and we're so happy," Vinales said.
Martin will be happy to have held off Oliveira to finish on the podium as he cut Bagnaia's lead atop the championship standings from 66 to 50 points.
"I started well, I tried to be calm in the first few laps even though Oliveira was pushing a lot," Martin said.
Martin also widened the gap to third-placed Marco Bezzechi (VR46 Ducati), who is 21 points behind the Spaniard after finishing 12th.
Earlier on Sunday, the race was red-flagged after Enea Bastianini slipped on turn one and took out Bezzechi, Johann Zarco, Fabio Di Giannantonio and Alex Marquez, before Bagnaia was launched into the air by a highside on the next turn.
Both Bagnaia and Bastianini were unable to return for the restart, leaving Ducati without a rider in the race.
