The Repsol Honda rider fractured a finger during a crash in morning warm-up but was passed fit to race.
Marquez, though, said he was ‘not ready' and instead suggested he will return to action at Assen.
“After five crashes, especially the one this morning [in warm-up], I don't feel ready to race, so I've decided not to push,” Marquez said in an interview with DAZN.
“Because in Holland there is more to come. I don't feel ready.
“I have many blows to my body and especially my ankle, a small fracture. I'm not ready.”
The 30-year-old has yet to finish a Grand Prix this season after seven rounds, with Marquez missing three GPs due to a broken hand following a crash at Portimao in Portugal in the season-opener in March.
His struggles with the factory RCV have come under increasing scrutiny, with Australian 500cc Grand Prix legend Mick Doohan saying Marquez needs to leave Honda to have a chance of winning a seventh MotoGP title, which would put him level with Valentino Rossi.
Marquez was unbeaten in a MotoGP race at the Sachsenring until Saturday's Sprint race, when he finished in a lowly 11th after enduring a difficult time throughout practice and qualifying.
During a nightmare weekend, he crashed at Turn 1 under braking in second practice on Friday, wiping out Johann Zarco in a horror collision that ripped the Frenchman's Pramac Ducati apart. Both riders escaped unscathed.
Marquez crashed a further three times over the course of Q1 and Q2 on Saturday, before his painful high-side at Turn 7 in morning warm-up made it five crashes in total.
On Friday, he showed his displeasure with the RCV, giving the finger to the machine in a moment of frustration after surviving a big moment at the fast Turn 11 Waterfall corner.
His withdrawal from Sunday's race left Japan's Takaaki Nakagami as the sole Honda rider on the grid, with Joan Mir absent due to a hand injury while LCR's Alex Rins was ruled out with a broken leg.
Nakagami, who suffered a hand injury in a crash on Friday, finished 14th in Sunday's race.