Making his sixth start since Tommy John surgery, Chatwood (4-2) struck out seven and walked one. Jake McGee pitched perfect ninth for his seventh save in eight chances, helping the Rockies win for just the seventh time in their last 27 games at Petco Park and avoid a three-game sweep.
Cesar Vargas (0-1) allowed one run, four hits and three walks in six innings.
Padres: RHP Tyson Ross, on the disabled list since April 5 because of inflammation in his pitching shoulder, has yet to begin his throwing program.
Rockies: LHP Chris Rusin (1-0, 1.69 ERA) is to face San Francisco on Thursday night in his second start this season. He didn't earn a decision Friday when he allowed one hit in five scoreless innings at Arizona.
Padres: RHP Colin Rea (2-1, 4.61) is slated to start Thursday night in the opener of a four-game series against the visiting New York Mets. Over his last four starts, Rea has gone 2-1 with a 3.13 ERA.