The defending NL West champions are 1-3 since their slugging left fielder was suspended Thursday for testing positive for a banned drug.
The Giants loaded the bases with one out in the 13th against Guillermo Mota (2-1), getting infield hits from Edgar Renteria and Steve Holm around a walk to Pablo Sandoval. Winn drove an 0-1 pitch into the left-field corner.
San Francisco took a 5-4 lead in the 12th on Rich Aurilia's bases-loaded sacrifice fly. The Dodgers tied it in the bottom half when Casey Blake drove a pitch from Brian Wilson into the former "Mannywood" seats in the left-field corner with one out, resulting in the right-hander's second blown save in nine chances.
Wilson (2-0) got the victory with two innings of one-hit ball.
Pierre, who two years ago played in all 162 games for the fifth straight season and lost his regular role when Joe Torre became manager last year, has started the last four games in left and is 9 for 16 with two walks, four RBIs, four runs scored and two stolen bases in that stretch.
Jeff Weaver was charged with two runs and three hits over five-plus innings. The Dodgers right-hander threw 76 pitches and departed after giving up a leadoff double in the sixth to Winn, who scored on a single by Emmanuel Burriss to cut the Dodgers' lead to 4-3. Burriss had a career-high four hits.
The Giants tied it at 4 in the eighth on pinch-hitter Nate Schierholtz's bases-loaded sacrifice fly.
Reigning NL Cy Young Award winner Tim Lincecum gave up four runs - three earned - and six hits over six innings after winning his previous three starts - including a 9-4 decision against the Dodgers on April 29 in San Francisco.
Pierre snapped a 2-all tie in the fifth with an RBI double to left-center after first baseman Travis Ishikawa turned Weaver's sacrifice attempt into a force at second. Pierre continued to third on a wild relay to the plate by shortstop Renteria and scored on a two-out double by Orlando Hudson.
The Giants took a 2-1 lead in the second on a bunt single, a hit batter, a sacrifice fly by Lincecum and three walks - one of them to Renteria with the bases loaded and two out.
Pierre scored the Dodgers' first two runs as a result of the added dimension his speed gives the team's already potent offense.
In the first inning, Pierre advanced from first to third on an errant pickoff throw by Lincecum and scored on Hudson's sacrifice fly. It was the first time in six starts this season that Lincecum allowed a run in the opening frame. The Dodgers have outscored their opponents 36-15 in the first.
In the third inning, Pierre stole second with two out and scored the tying run on Rafael Furcal's single.