The German sprinter won both road stages in the Netherlands to start the Giro last Saturday and Sunday but was unable to replicate his early form when the race moved on to Italy from Tuesday.
Another brutally tough stage on Saturday saw Kittel finish in a group with many of the other sprinters, 18 minutes down on his teammate and stage winner Gianluca Brambilla.
"Considering from where I came it's very important for me to pay attention to my fitness level. The Giro has been a tough and demanding race so far, even in the stages bookmarked for the sprinters," Kittel said.
"Now I feel that I need to rest before the future goals of the season. I leave from here with a brace of wins and with many great memories, two of which are wearing the pink jersey for the first time in my career and the great ride of Gianluca Brambilla on Saturday."
Kittel is likely to target stage wins and the yellow jersey at the Tour de France in July.
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