"He was on pace to play 155 [games]," Pirates manager Clint Hurdle said.
Nate McLouth started in center for the first time this season.
McCutchen, who has hit safely in seven of his last eight games, sports a .377 lifetime average in St. Louis.
"You never want to sit out," McCutchen said. "But I'm sure it's going to benefit me later on. Nothing wrong with taking a game off every once in a while."
McLouth, who is making his fifth start this season, has been struggling, entering the game with a .174 average. He is 0-for-8 as a pinch-hitter.
"I've been getting beat on pitches that I shouldn't be getting beat on," McLouth said. "Maybe this will help. Get a few hits, get things going."