The Dutchman crashed on stage four of the race, injuring his knee, and eventually abandoned just 1.5km into stage five the following day.
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Dumoulin then returned to racing at the Critérium du Dauphiné but abandoned before the final two mountain stages with the plan of heading to an altitude training camp in the Alps.
Due to arrive on Monday, the 28-year-old turned around after beginning his drive to the camp, unsure if he was ready or not to begin working for the Tour de France, starting on July 6 in Brussels.
He and his Sunweb team have now confirmed that he will not take part in the Tour, saying that with his condition it is not realistic for him to be competitive.
“The last month has been extremely difficult overall, and with the setbacks in the knee recovery,” Dumoulin said.
“After what happened at the Giro I really wanted to go for it in the Tour, but this week I realised it’s just not realistic for my level to be there in time. I’ve tried so hard to get there but I really have to listen to my body and release myself from chasing an unrealistic goal.”
With just over two weeks until the Tour begins, there is little time for Dumoulin to turn his form around ahead of the race, where he would come up against the likes of Geraint Thomas and Egan Bernal (Team Ineos), Nairo Quintana (Movistar), Adam Yates (Mitchelton-Scott), Romain Bardet (Ag2r La Mondiale), Jakob Fuglsang (Astana) and Thibaut Pinot (Groupama-FDJ) in a route heavy on high mountains and low on time trials.
Team Sunweb physician Anko Boelens said there have just been too many setbacks since crashing out of the Giro for Dumoulin to be ready in time for the Tour.
“Tom was really eager to be ready in time for the Tour and he tried all he could, but now the conclusion is that it’s simply not possible,” Dr Boelens explained.
“We trusted in the process of rest, recuperation and a gradual return to racing but like in any recovery, there have been setbacks.
“Time isn’t on our side anymore to cater for setbacks so to give Tom the time he needs to get back to complete fitness can only be the right decision. Despite his strong will and ambition to race the Tour it’s better to let this goal go this year in favour of optimum recovery.”
The Tour de France has now lost two of its big favourites for general classification with Dumoulin missing, with Chris Froome also out following his horrific crash at the Dauphiné.