He scored later in the frame on a two-run single by Ben Zobrist.
Lester pitched two scoreless innings. He allowed a leadoff single in the third, and after two pitches to the next batter, was checked by manager Joe Maddon and the team's trainer.
He was pulled with the Cubs holding a 6-0 lead against the Pirates.
Last season, Lester he was 18-6 with a 3.32 ERA in 32 starts. In two starts this, season he has allowed four runs in 12 innings and had a 1-0 record.
Brad Brach came in to relieve Lester.