Daubach's double on a 2-2 pitch off Armando Benitez (2-4) hit the base of the right-field wall, scoring Manny Alexander and Jose Offerman. Alexander pinch ran for Scott Hatteberg, who walked. Offerman reached on an error by shortstop Melvin Mora on what could have been the game-ending double play.
Rich Garces (4-0) got the win with 1 1-3 innings of scoreless relief.
Benitez blew his fourth save in 23 chances.
Martinez left his first start in 18 days with a no-decision after striking out 10 and allowing two runs in seven innings.
Boston scored just two runs for their ace, continuing a recent trend of anemic offense when Martinez is on the mound. His league-leading ERA increased from 1.44 to 1.51.
Mets catcher Mike Piazza delivered a key hit in his first game back after being beaned by Roger Clemens.
Piazza's single with two outs in the eighth inning off Garces was misplayed by center fielder Carl Everett, allowing Edgardo Alfonzo to score from first. Alfonzo singled off reliever Rheal Cormier.
Piazza was knocked out of last Saturday's game with the New York Yankees and forced to miss the All-Star game after he was hit in the head by Clemens' fastball.
Mets starter Bobby J. Jones cruised early, striking out eight in the first five innings, and bearing down when he got in trouble.
After Troy O'Leary doubled with one out in the second, Jones struck out the next two batters. When Nomar Garciaparra singled and stole second leading off the fourth, Jones fanned the next three.
The Mets took an early lead off Martinez when Jay Payton followed Todd Zeile's two-out double with a double down the third-base line in the second.
Boston went ahead in the sixth on Morgan Burkhart's two-run homer following Everett's single, but Payton tied the game 2-2 with a solo shot into the left-field screen in the seventh.
New York's defense came up big in the eighth when Zeile stopped O'Leary's one-out smash down the right-field line, preventing Garciaparra from scoring from second. John Franco then struck out Burkhart to end the inning.
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