The San Francisco Giants scored three runs in the top of the ninth inning to tie the game 4-4.
But the New York Mets came back in the bottom half and loaded the bases only to score the run on a throw away by Buster Posey.
The Giants lost the game 5-4 after winning a ten inning thriller the night before.
San Francisco (7-7) has won six of eight and three in a row after opening the four-game series with a 4-3 victory in 10 innings Friday.
Friday night's loss was the third in a row for New York (7-7) after winning seven of its first 10.
Saturday the Mets were able to reverse their fortune after leading 4-1 going into the ninth and blowing the lead.
Posey started the Giants' ninth inning rally with a single. Nate Schierholtz drew a one-out walk and Emmanuel Burriss hit an RBI single up the middle.
Then manager Bruce Bochy used Brandon Belt as pinch-hitter. He was rewarded when Belt hit a two-run double, tying the game for the Giants.
But the Mets struck back in the bottom half of the inning. New York loaded the bases before scoring on Posey's throwing error to first base.
Posey argued that he had been obstructed at home plate when making the throw to first, but the umpire ignored his pleas.
The strange game was highlighted by Aubrey Huff playing second base for the first time in his career in the bottom of the ninth. Huff made a mental error before the Mets scored the winning run when on a routine double ball he shifted towards first instead of covering second.