Rookie Freddie Freeman doubled twice to run his hitting streak to 19 games, a personal best. Hudson (11-7) allowed three hits in helping the Braves hand the Mets their fifth straight loss.
Jose Constanza had an RBI triple and Michael Bourn a sacrifice fly for Atlanta off R.A. Dickey (5-10). Constanza made two acrobatic catches on drives by Jose Reyes in left field and Jason Heyward made a diving grab on Daniel Murphy's drive in right.
The Mets have not scored more than three runs during the skid that dropped them below .500 for the first time since July 18. More pressing, New York fell nine games behind the wild card-leading Braves.
They put runners on first and second against Jonny Venters in the eighth but came up empty. Craig Kimbrel was perfect in the ninth for his 33rd save.
Hudson did not allow more than three runs for his 11th straight start, improving to 7-2 in that span. On June 5 he gave up five runs against the Mets.
He retired nine straight after David Wright's RBI double high off the wall in left-center. Angel Pagan's two-out walk in the fourth ended that stretch, and Jason Bay's ground-rule double and Lucas Duda being hit with a pitch loaded the bases.
Josh Thole then popped out, falling to 1 for 9 with the bases full and two outs.
Despite another sold outing, Dickey lost his 10th game for the first time in his career. Other than a shaky third, the knuckleballer gave the Braves little opportunity to break open the game.
In the sixth, Martin Prado singled with one out and moved to third on Freeman's double. But Uggla struck out with a mighty cut and was 0 for 3 against Dickey — he dropped to 0 for 18 against him for his career. Heyward grounded to short to end the threat.
Dickey gave up five hits and two runs. He struck out five without walking a batter.
Uggla got his two-run single off Ryota Igarashi in the eighth.
Duda hit a drive leading off the seventh that got a rise out of the crowd at Citi Field but it fell into Heyward's glove just in from of the wall in right-center of the expansive ballpark.
Getting the call from the minors last week when Nate McLouth went on the disabled list, Constanza ripped a liner into right-center that drove in Alex Gonzalez for the first run. Constanza stumbled around third when he was held up at the last second for a triple.
McLouth had sports hernia surgery on Thursday and will be out at least six weeks, offering Constanza steady playing time.
Bourn hit a sacrifice fly to left for the 2-1 lead.
Notes: The Mets wore blue jerseys with "Los Mets" written across the chest in honor of Fiesta Latina Night. ... Braves 3B Chipper Jones (tight right quadriceps) was held out of the Braves lineup for one more game. He said he was ready to play but Atlanta held him out as a precaution. Jones should start Saturday. He will rest Sunday because he's been limited to pinch-hitting duties since returning from arthroscopic surgery on June 25. ... Mets 1B Ike Davis (bone bruise, left ankle) is likely done for the season. Out since getting hurt May 10, Davis will stop running for four weeks before being reevaluated. ... Braves OF Eric Hinske turned 34 Friday.