Hernandez didn't give up an earned run -- Atlanta took advantage of two New York errors -- and he also picked up the first two RBI of his career during a seven-run sixth that broke open a 3-all game.
Beltran capped the big inning with a three-run homer off Chad Paronto, who had just replaced starter Tim Hudson. The Mets center fielder also hit a two-run shot in the first and now has 30 homers for the year -- 14 more than he did during a disappointing first season in New York.
"I just want to stay healthy," he said. "If you're not healthy, you can't accomplish much. The difference between this year and last year is I have been healthy."
Endy Chavez chipped in with three RBI for New York, which outhit the Braves 15-4.
Hernandez (7-8) won his third straight decision and further solidified his spot in the Mets' shaky rotation, their only major area of concern as they go for their first playoff appearance since reaching the Subway World Series in 2000.
"I'm not thinking about the postseason yet," El Duque said. "I'm staying ready for tomorrow. The postseason is way in the future."
The Mets, four times a runner-up to Atlanta in the East, now hold a commanding 14-game lead on their rival, which had hoped to use the weekend series to boost its flagging hopes of winning a 15th straight division title.
Instead, the Braves suddenly resemble the team that won only six games in June. After winning six straight series to get back into the wild-card race, the Braves have lost four of five at home.
"This ain't exactly how we wanted this series to start out," Hudson said. "We've just got to put these two games behind us and try to salvage one."
On Sunday, the Mets will go for their first sweep of at least three games in Atlanta since 1985.
It was another rough outing for Hudson (8-9), who gave up nine earned runs to equal the worst showing of his career. He allowed 10 hits in 5 2/3 innings, leaving the field to a round of boos from another big crowd at Turner Field as his ERA climbed to 5.25.
Since scoring four runs off Pedro Martinez in the first inning Friday, Atlanta has only five hits over the last 17 innings against the Mets -- including a 2-for-45 stretch.
Hudson stumbled in the beginning but appeared to be settling down with three straight scoreless innings. Then came the sixth.
Struggling with his control, Hudson walked David Wright, gave up a single to Cliff Floyd and let both runners move up with a wild pitch. After Hudson walked Jose Valentin intentionally to load the bases, Chavez's two-run single put the Mets ahead for good.
Then came the killer for Hudson. His counterpart, batting for only the 30th time in a career spent mostly in the American League, singled up the middle to drive in two more runs and push the Mets to a 7-3 lead.
Asked if he remembered his last RBI, Hernandez said, "I think it was in Cuba."
Hudson's third walk of the inning finally brought manager Bobby Cox out of the dugout to lift his starter. But Beltran got hold of Paronto's third pitch, sending a drive into the right-field seats that sent many in the sellout of 49,047 scurrying for home.
"I thought I threw some pretty good pitches, but they hit them," Hudson said. "You've got to tip your cap to them. They're a good ballclub."
He might be giving the Mets a little too much credit. Over his last nine starts, Hudson is 2-5 with an ERA of 8.87. He has allowed 70 hits, eight homers and 23 walks during that stretch of 44 2/3 innings.
"Obviously, this is something no one wants to go through," Hudson said. "I feel good. It's almost like the other team knows what I'm going to throw sometimes."
The only downer for the Mets: First baseman Carlos Delgado left the game in the third after getting struck on the right knee with a pitch from Hudson. But X-rays were negative and he was day to day with a painful bruise.
The Mets started the game with three straight hits off Hudson, including Beltran's homer to right-center. The Braves mitigated the damage somewhat by throwing out Jose Reyes attempting to steal.
Atlanta scored in the bottom half after Wright messed up a likely double play with a high throw from third base.
Chavez hit a run-scoring triple in the second, but Marcus Giles tied it up with a two-out, two-run single in the Braves' half. Reyes kicked away a grounder at shortstop to extend the inning.
- Hernandez picked up his second regular-season win against the Braves, the first coming on June 2, 2000, when he allowed one run in seven innings for the Yankees.
- Beltran had the 16th multihomer game of his career and third this season.
- Hudson allowed nine earned runs in a game two other times, most recently on May 4, 2002, while pitching for Oakland.