The NLDS would be a close, hard fought series between the two teams. Tim Lincecum would toss a complete game two hit shutout and strike out a franchise postseason record 14 in the opener as the Giants won 1-0. In game two, the Giants took a 4-0 lead behind Matt Cain. But the Braves fought back, tying the score with three runs in the eighth, then winning in the 11th inning 5-4 on Rick Ankiel's home run as the series shifted to Atlanta.
In game 3, Jonathan Sanchez was brilliant, striking out 11 and carrying a no hitter into the sixth inning. The Giants led 1-0 in the eighth inning before Eric Hinske hit a two run home run to give the Braves the lead. Rookie right-hander Craig Kimbrel came out of the bullpen to start the top of the ninth for the Braves, relieving Jonny Venters who had struck out the side the previous inning. Kimbrel retired Cody Ross on a popout to Brooks Conrad, for the first out. Travis Ishikawa then pinch-hit for Sergio Romo and drew a walk. After striking out leadoff man Andrés Torres, Kimbrel gave up a single to second baseman Freddy Sanchez, and was removed from the game, leaving runners on first and second base, with two outs. Another rookie Brave, lefty Michael Dunn came on and gave up a game-tying single to Aubrey Huff. Dunn was then pulled for a right-hander, Peter Moylan, who induced a grounder from Buster Posey, which proceeded to bounce through the legs of Conrad, the second baseman's third error of the game. Sanchez scored on the play, giving the Giants a 3–2 lead. Kyle Farnsworth came on and got the third out, but the damage was done. The Giants brought in their closer Brian Wilson for the bottom of the ninth. He held the lead, giving up a single to Brian McCann but retiring Nate McLouth on a grounder to end the game.
With their backs against the wall, the Braves sent Derek Lowe to the mound on three days' rest. The Braves scored first in the bottom of the third inning when Brian McCann's sacrifice fly drove in Omar Infante.
Lowe took a no-hitter into the sixth inning, but the Giants tied the game with one out on Cody Ross' first-pitch homer off a Lowe cutter. Brian McCann answered with another in the bottom of the inning off the Giants' rookie starter, Madison Bumgarner, to take back the lead. Lowe was relieved after 6 1⁄3 innings. After walking Aubrey Huff and allowing an infield single to Buster Posey, Bobby Cox made his way out to the mound, apparently to remove Lowe from the game. However, after talking to him, Cox elected to leave Lowe in, prompting huge cheers from the Atlanta fans.
The next batter, Pat Burrell, walked on a 3–1 pitch near the inside corner and Lowe's night was done. He struck out eight while allowing only two hits and walking two. Braves' relievers Peter Moylan and Jonny Venters could not hold the lead as the Giants scored two runs in the top of the seventh inning on Juan Uribe's RBI fielder's choice and Cody Ross' RBI single. The Braves might have been able to escape the one-out, bases-loaded jam, however, Álex González's throwing error, his second in the game, cost them. Both errors were debatable. The first, was a ball hit in the hole he didn't field cleanly with the speedy Andrés Torres running. The second, was again, another crucial controversial call that went against the Braves in the series. With two on and one out and a weakly hit groundball, González elected to go to second, throwing it high, causing Omar Infante to edge up, however, the umpire ruled he came off the base.
Left-handed Giants reliever Javier López entered the game with two outs in the eighth, and pinch-runner Nate McLouth as the tying run at second base, and struck out Jason Heyward. In the bottom of the ninth inning, the Braves had one last chance to rally. With one out, Giants closer Brian Wilson walked Rick Ankiel and Eric Hinske to put the winning run on base. However, Omar Infante struck out swinging and Melky Cabrera grounded out to end the game and the series in what would be Cox's final game. Both teams would give Cox a standing ovation following the final out.