LaTroy Hawkins (2-0) pitched a 1-2-3 ninth and has not given up a run in 10 outings since Houston acquired him in a trade with the Yankees on July 30. Hawkins had a 5.71 ERA with New York.
Jose Valverde worked a perfect 10th for his 33rd save in 39 tries.
Pedro Feliciano (2-4), the Mets' sixth pitcher, gave up both home runs in the 10th and New York lost consecutive games for the first time since Aug. 10-11. The NL East leaders fell to 1-5 against Houston this season.
Oliver Perez was pulled after walking Pence with one out in the seventh, and the Mets' bullpen reverted to its struggling ways after showing signs of stabilizing during the first five games of a seven-game homestand.
Aaron Heilman gave up a double off the right-field wall to pinch-hitter Geoff Blum on his first pitch. With slugger Lance Berkman being given the day off after a night game to rest his sore left hamstring - he batted in the 10th - pinch-hitter David Newhan then singled to right to drive in Pence, but Blum was nabbed trying to score. Fernando Tatis' throw to catcher Ramon Castro beat Blum by several feet to keep it tied at 4.
Heilman, who hadn't allowed a run in four outings, did not move from the stretch position while manager Jerry Manuel made the walk from the dugout to replace him with Scott Schoeneweis.
Pinch-hitter Michael Bourn walked but was stranded when Reggie Abercrombie grounded out.
Beltran gave New York a 4-3 lead with his second homer of the game, a drive off the screen attached to the left-field foul pole.
Beltran, a switch-hitter, had hit just two of his 17 homers from the right side before connecting as a righty twice against Mets nemesis Randy Wolf.
It was Beltran's 24th career multihomer game and second this season.
Beltran's first homer came after David Wright walked in the first. Jose Reyes singled leading off but was thrown out at second trying to tag up on a fly to left-center.
Wolf got help from his defense in the third, too. After Tatis walked with the bases loaded to make it 3-0, second baseman Loretta made a diving catch of a flair hit by Damion Easley near the line in shallow right, sliding on his belly and holding his glove up, with plenty of ball showing, to end the threat.
Loretta then hit a sacrifice fly in the fourth, and Pence, who came in hitting .190 (15-for-79) in August and looked lost striking out in the second, hit his career-high 18th homer, a two-run shot that tied it 3-all.
