The four-time World Champion suffered a hefty fall on the second of three runs.
But having initially tried to land on his feet, he rolled and then sprinted for a lift back to the paddock.
He hitched a ride on a moped and a marshal dropped him off back at the Honda garage.
The Catalan ace then fired up his second bike to complete his qualifying run.
Speaking after the incident, Marquez said: “I lost the front early, where I didn’t expect it, because I leaned the bike too aggressively and then I was not ready [to save it] with the elbow.
“Of course I tried to save it, but when I saw the gravel, the wall, approaching, I checked a bit and then just put my arms on my shoulders, which are very important to protect.
“My other saves were crashes that normally you can control, but this was a big crash and it’s important to be fit.”
Marquez, 25, has previously suffered serious injuries to his shoulders.
From crashing to getting on his second bike took Marquez just two and a half minutes.
The Honda man says his remarkable turn of pace even surprised him.
He added: ”It was so quick. Even the guy with the scooter was pushing a lot, it was scary sometimes that we would crash, but he did a great job!
“It surprised me [how quick] because when I took the second bike I thought, ‘okay, there will be time to do one lap’.
“But I was able to do two laps. It [getting back to the pits] was even faster than a normal in-lap with the bike!”
Jorge Lorenzo starts the race in pole position.
Yamaha superstar Valentino Rossi is seventh on the grid.
San Marino Grand Prix starting grid: