Midfielder Ramiro Corrales and forward Kei Kamara scored on either side of halftime to overcome a goal in the fifth minute by Darren Spicer.
With two wins in two games, San Jose clinched the top spot. In the first game of a doubleheader, New York and Toronto FC tied, 1-1, with John Wolyniec and Jeff Cunningham, respectively, netting the goals. Since neither team had won its opener, neither could catch the Quakes even by winning their final games on Saturday.
San Jose limited Charleston to four shots on goal and two quality scoring chances, justifying Coach Frank Yallop's decision to build his expansion team from the back.
"From day one I thought we would be organized and difficult to break down," Yallop said. "When we do the right things in the back we're going to be a hard team to play against."
Conditions had improved since last Saturday, when a game in which San Jose led Toronto, 1-0, as rain and wind lashed Blackbaud Stadium had to be suspended in the 77th minute and then called off when a lighting storm struck the area. Still, strong winds buffeted the players in the first half, and a torrential downpour fell in the second period.
Quakes keeper Preston Burpo couldn't deal with a wind-whipped corner kick and when an attempted punch fell to Spicer he knocked it home. San Jose equalized when Corrales ran onto a pass from Ned Grabavoy and shot past Battery keeper Keith Wiggans to tie the game in the 26th minute, and in the 70th minute Corrales played the through ball that Kamara took uptown for the winner.
"Ramiro is a really good footballer," Yallop said of the veteran who returned to MLS in January following a stint in Norway. "He's done very well for us in the middle of the field."
Juan Pablo Angel nearly stole a win for Red Bull New York with 10 minutes to play but his shot hit the goalpost. Earlier, a tangle of Angel and TFC defender Julius James resulted in the rookie leaving the game with a shoulder injury.
Toronto plays the Battery Saturday in the first game, with New York and San Jose set to conclude the event.