The 24-lap race on Sunday in Barcelona was halted after two major incidents in the first two corners, one of which involved Bagnaia.
The reigning champion got the holeshot from pole position and crashed on his own as he came around Turn 2.
Bagnaia was then sickeningly struck by KTM’s Brad Binder, who could do nothing to avoid running over the Ducati rider’s leg.
The race was immediately red-flagged as Bagnaia received instant medical attention.
He was taken to the medical centre by ambulance and was reported as conscious before being transferred to Hospital General de Catalunya.
Bagnaia looks to have largely escaped any serious injuries, with the Italian undergoing scans to confirm he has not suffered any fractures to his leg.
Bastianini, meanwhile, is thought to have suffered fractures to his hand.
The first crash was instigated by Ducati’s Enea Bastianini, who crashed on the way into Turn 1, triggering a collision with Pramac Ducati’s Johann Zarco.
This then involved both Gresini Ducati’s of Fabio Di Giannantonio and Alex Marquez, and the VR46 Ducati of Marco Bezzecchi.
Bastianini did not take the restart having gone to the medical centre for checks, meaning no factory Ducati team rider will be present in the Catalan GP.
He was then transferred to hospital alongside his team-mate.
It is not clear yet how the stewards will impose his long lap penalty, as the punishment was handed out for this race.
All the other riders involved appeared to walk away unscathed.
A quick restart procedure began at 2:21pm local time, where pitlane was open for 60 seconds.
Riders made their way to the grid, where they were met by one mechanic before being sent off on a sighting lap.
Aleix Espargaro went on to win the race from team-mate Maverick Vinales in an historic 1-2 for Aprilia, with Pramac Ducati's Jorge Martin in third.
He dedicated his win to Bagnaia, and said in parc ferme: “I’m speechless.
“First thing I want to say is I’m happy, really, really happy that nothing [serious] happened today on the first start.
“Lucky that Pecco is nothing really serious, they told me now. So, this win is for Pecco because I was just behind, I was very worried.
“Then I tried to reset my mind and for the riding style we do, this win was very difficult because I let the bike flow in the mid-corner and the wind pushed me out.
“Maverick is a lot stronger at stopping the bike and going. It was difficult for me to follow, I made a mistake when I was trying to overtake and then I lost a lot of ground.
“I thought for a moment I wouldn’t catch him, he was very fast. But I changed [engine] map and I went to the limit, like qualifying, for 25 minutes and I’m very happy.”
