Dowsett made his Tour debut last year and was part of the Spanish team's long list of 13 for this year's race, but he will not be in the nine that start in Mont-Saint-Michel.
"He won the national time trial, but he's not in great form. He's in good form, but not great," team manager Eusebio Unzué told Cycling Weekly.
"We wanted a cyclist in our nine-man team who is more complete than he is. We needed riders who were less a time trialer and ones who could go well on the flats and climb well."
Quintana named Dani Moreno, Winner Anacona and Alejandro Valverde, third overall last year, as his mountain men. Unzué said that without Dowsett, they would still have support in the flats for Quintana with Nelson Oliveira, Imanol Erviti and Jon Izagirre, winner of the Tour de Suisse time trial.
Watch Cycling Weekly's guide to the opening stages of the 2016 Tour de France
Dowsett explained last week that he expected to be overlooked given how he rode in the Tour de Suisse.
"I was really under par," he said. "It's a lack of top end form. It's a misjudgment in training. I have done a lot of threshold stuff and my time trialling at the moment is good but I've neglected the top end."
The Brit could yet start in the Vuelta a España later this summer, but Unzué explained that the priority is to ride in the worlds time trial in Doha, Qatar.
Quintana has finished second to Froome in both of his previous appearances in the Tour, in 2013 and 2015. Last year, he nearly toppled Froome in the final week, but suffered from losses in the first road stage and on the first summit finish to Pierre-Saint-Martin.
"Froome's weakness? I don't know, maybe that he's under condition in the third week normally, but now I hear that he prepared well for it, so that could change," Quintana said.
"I have trained to be able to be able to respond to his strong attacks. When he starts, though, it's difficult to stop him. As we saw in Pierre-Saint-Martin last year, I couldn't follow him. I hope this year I'll be able to be follow him all the time."
More on this year's Tour de France
Quintana's season has been more successful in the top races this year than Froome's. So far, the 26-year-old won the Vuelta a Catalunya, the Tour de Romandie, and the Route du Sud. Froome has won the Herald SunTour and Criterium du Dauphiné.
"I don't know if I feel stronger than last year, but at least I feel more relaxed," added the Colombian. "I know I have great condition, my rivals too, but I felt really well and positive in all the races so far this year."
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