SAN DIEGO – Derrek Lee slid home safely with the go-ahead run on the first of two run-scoring groundouts in the ninth inning and the Chicago Cubs beat the San Diego Padres 3-1 on Thursday night.

Lee led off with a single off Cla Meredith (1-2) and went to third on a single by Aramis Ramirez. Cliff Floyd then hit a two-hop grounder to second baseman Marcus Giles, who threw home to try and get Lee. But Lee did a hook slide around catcher Josh Bard to give Chicago a 2-1 lead.

The Cubs loaded the bases on Michael Barrett’s bunt single. After Heath Bell replaced Meredith, pinch-runner Angel Pagan scored on Ryan Theriot’s groundout.

Bob Howry (2-3) pitched a perfect eighth for the win. Ryan Dempster got his 10th save in 11 chances by working a perfect ninth.

Lee, the NL batting leader at .370, got his first hit in 12 at-bats since he returned to the Cubs’ lineup on Tuesday. Lee had been out of action since May 13 with neck spasms.

Chicago beat the Padres for the second time in 12 games, dating back to last year.

San Diego’s Chris Young retired the first 12 Chicago batters until he gave up a leadoff double in the fifth to Ramirez. Barrett followed with a one-out double to tie the score at 1.

The run was only the second earned run allowed by Young in four home starts covering 27 1-3 innings. Young allowed one run and three hits in seven innings. He struck out a season high 10 batters with two walks.

Adrian Gonzalez led off the San Diego second with a double and scored one out later on Josh Bard’s single for a 1-0 lead.

Alfonzo Soriano tripled into the right-center field gap leading off the sixth.

But Young then struck out Mark DeRosa, Lee and Ramirez to get out of the jam.

Jason Marquis matched Young as he allowed up one run on five hits over seven innings. Marquis walked three and had five strikeouts.