Henry Rodriguez opened the 11th with a double off Aaron Fultz (1-1).
Pinch-runner Chad Meyers moved to third on a groundout and, after a walk, scored on Nieves' fly to right.
Daniel Garibay (1-1) pitched two hitless innings for the win. Rick Aguilera pitched the 11th for his eighth save in 12 opportunities.
After being held scoreless on one hit for the first 7 2/3 innings, the Cubs tied the game at two on back-to-back homers by Rodriguez and Julio Zuleta off reliever John Johnstone.
Rodriguez's 12th homer of the season went into the seats above the brick wall in right-centre.
Zuleta's first major-league homer, capping a 12-pitch at-bat, went to left-field.
The two homers deprived San Francisco starter Russ Ortiz of a win after a roller-coaster performance in which he allowed one hit in six scoreless innings -- striking out a career-high 11 and matching his career high with seven walks.
Ortiz allowed only a double by Willie Greene in the fifth.
He struck out the side in the fourth and fifth innings, got Sammy Sosa twice on strikes and whiffed Zuleta three times.
