Jones also homered in the first inning and Pittsburgh managed only four other hits until he drove an 0-1 pitch over the wall in right off Bob Howry (0-5).
The Pirates halted a four-game losing streak and handed the Giants their second straight setback.
San Francisco tied it in the seventh when Randy Winn raced in from third on a two-out fielding error by second baseman Freddy Sanchez. That miscue spoiled a sensational effort by starter Paul Maholm, who allowed four hits and struck out seven over eight innings.
Maholm battled San Francisco ace Tim Lincecum on even terms. Lincecum, who had been seeking his 11th victory, gave up five hits and fanned 10 in seven innings.
The win went to Evan Meek (1-0), the seventh Pittsburgh hurler who worked the top of the 14th.
Copyright 2009 by United Press International.