Marquez suffered a high-side at the Turn 5 left-hander at the end of the first qualifying segment.
The 27-year-old immediately threw off his right glove and took some time to get to his feet, before needing to be helped away by the marshals.
Despite progressing into Q2, Marquez was unable to compete in the session as he was taken to the medical centre for checks.
Initial examination discovered potential rib fractures before he was taken to a hospital in New Delhi for further checks.
Scans ruled out any serious injury, but he has suffered fractures to his sixth, seventh and eighth ribs on the left side of his body.
This has forced him out of Saturday's sprint at the Indian GP and Sunday's main race.
And with the Japanese Grand Prix just a week away, it is likely Marquez will also be absent from the Motegi round.
Marquez was due to start both races at the Buddh International Circuit from 12th, meaning that everyone who qualified behind the Gresini rider will move up one place following his withdrawal.
Alex Marquez came to India ninth in the standings on 108 points having scored a podium at the Argentina GP and won the sprint contest at Silverstone.
He will remain with Gresini Ducati next season, with the identity of his team-mate MotoGP's biggest story right now as rumours persist that his eight-time world champion brother Marc Marquez could break contract with Honda to join him.
Ducati already came to India with a depleted roster, after Enea Bastianini fractured his left hand and ankle in a Turn 1 smash at the Catalan Grand Prix earlier this month.
Having undergone surgery on his injuries, Bastianini was ruled out of the San Marino, Indian and Japanese GPs.
He is being replaced by Ducati test rider Michele Pirro in India.
LCR Honda's Alex Rins is also out of action this weekend as he continues to recover from the leg he broke in a crash at the Italian GP back in June.
