Hairston connected on a 3-1 pitch from Pedro Feliciano (0-1) into the left-field seats to give San Diego its season-high fourth win. Beginning with their 12-9 win in 18 innings on May 25 against Cincinnati, the Padres have won nine of 13.
Mke Adams (1-0) pitched the 10th inning for the win.
San Diego has played eight extra inning games, including five that lasted 13 or more innings.
The Mets lost their third straight game after having won seven of their previous 10.
Before Friday night's 2-1 win over New York, the Padres had never won more than two straight 2-1 games in their 40-year history. The Padres started their streak with a 2-1 win over the Chicago Cubs on Wednesday night.
The Mets jumped in front 1-0 on a sacrifice fly by Endy Chavez in the second inning.
Michael Barrett tied the game with a leadoff homer in the fifth off Oliver Perez, his first in more than a year. Barrett's last home run came on June 10, 2007, at Atlanta when he was with the Chicago Cubs, a span of 197 at bats.
New York worked out of two bases loaded jams.
The Padres loaded the bases in the fourth inning on a leadoff walk to Edgar Gonzalez, Brian Giles' infield single and a two-out walk to Khalil Greene. But Perez got Justin Huber to line out to right field.
In the sixth, Perez hit Giles with a pitch to lead off the inning. Perez then hit Kevin Kouzmanoff one out later. Joe Smith replaced Perez and proceeded to hit Greene to load the bases. Smith retired pinch-hitter Tony Clark on a forceout at the plate and struck out Barrett.
The three hit batters in the inning tied a major league record.
It was the second time in Mets' history they have hit three batters in an inning. Perez plunked three Florida Marlins last season in a 7-4 loss on Sept. 28 as the Mets dropped out of first place behind Philadelphia. New York finished one game behind the Phillies as they squandered a seven-game lead with 17 games left.
Carlos Beltran and Carlos Delgado had consecutive singles to lead off the New York second with Beltran going to third. Fernando Tatis then hit a grounder to third base. When Beltran broke for home, Kouzmanoff threw home to Barrett. Beltran was able to get back to third with all the runners being safe.
Beltran then scored on Chavez's sacrifice fly.
Perez allowed one run and four hits in 5 1-3 innings. The former Padre struck out five, walked two and hit two batters.
Cha Seung Baek gave up one run and seven hits with two walks and two strikeouts in six innings.
Notes: Mets OF Ryan Church sat out his second straight game and will not play in Sunday's finale because he says he is "not feeling right". ... New York reinstated C Raul Casanova from the bereavement list. The Mets optioned C Robinson Cancel to Triple-A New Orleans.
