Kittel, winner of stage seven, had always planned to leave the Vuelta early according to team manager Rudi Kemna, and will now focus on his preparation for the UCI Road World Championships at the end of the month.
"This is entirely according to plan," confirmed Kemna. "Marcel is still young and you should eventually be better off if you're in a race as it goes on. He can take a rest."
Kittel's fatigue was evident on Thursday, dropped with 10 kilometres to go before being brought back to the bunch by his teammates.
"They have helped me very well," the German said. "But I just was not strong enough to stay in position at the front with the best sprinters." He eventually crossed the line in 81st, 34 seconds off the pace.
"I am not glad to have to leave the Vuelta," Kittel admitted. "I have had two wonderful weeks and would like to thank the organization for inviting us. To get a victory in my first grand tour is unbelievable."
It's been a successful year for the 23-year-old, who prevailed in the fifth stage of the Tour de Langkawi, won four stages at the Four Days of Dunkirk, won the first stage and then overall at the Delta Tour Zeeland, before claiming four stages at the Tour of Poland.