John Maine pitched five effective innings and David Wright snapped out of a slump with two hits for the Mets, who had lost five of six.
Atlanta dropped to 0-8 in one-run games and is the only team in the majors without a win in that situation. They had to play without Chipper Jones, who was a late scratch after feeling spasms in the middle of his back in the clubhouse before the game. Jones, a career .310 hitter at Shea Stadium, was leading the majors with a .433 batting average entering play Saturday.
Prado's RBI single off slumping right-hander Aaron Heilman cut it to 4-3 in the sixth. But four Mets relievers combined to throw three scoreless innings, as New York earned its first win in four games against Atlanta this year.
Billy Wagner worked the ninth for his fifth save in five opportunities. Prado led off the ninth with a deep drive to center but Beltran caught it on the warning track.
Atlanta had been leading 2-0 before New York rallied in the third. Endy Chavez singled with one out and Wright broke an 0-for-19 skid with a hit to right, putting runners on first and second. Beltran then hit a long drive over the head of center fielder Mark Kotsay. Chavez scored easily and Wright slid in just ahead of catcher Brian McCann's tag. The All-Star third baseman hopped up and pumped his right arm after narrowly beating the throw home.
Ryan Church tripled in Beltran and scored on Carlos Delgado's groundout to make it 4-2. New York nearly had its first five-run inning since April 2, but Prado made a leaping grab of Gustavo Molina's liner with a runner on second for the final out.
That was the final inning for Tim Hudson (3-2), who allowed seven hits and threw just 60 pitches in another perplexing start. The right-hander lasted just three innings at Florida on April 16, struggling with the velocity on his fastball, but bounced back with 6 2-3 innings in a win against Washington on Monday.
