The loss is the 82nd of the season for Pittsburgh. The Pirates are guaranteed a 17th consecutive losing season, breaking the record the team shared with Philadelphia, which had 16 straight losing seasons from 1933-48.
Lee has five home runs in his last four games. Milton Bradley drove in the Cubs' other run.
Ted Lilly (11-8) got the win after giving up just two runs on two hits in six innings.
Andy LaRoche hit a solo home run and Brandon Moss drove in the other run for the Pirates, who have lost 10 of their last 11 games.
Daniel McCutchen (0-1) lost the second start of his career after being charged with four runs on nine hits over seven innings.
Copyright 2009 by United Press International.