Bumgarner (12-7) gave up just three hits in six innings. He struck out seven and walked one in posting his sixth successive quality start.
Bumgarner has given up 18 homers this season, 15 on the road.
Yet he says the pitch that Beltran hit for his 27th homer of the season was not a bad offering.
"It was pretty much right where I wanted to throw it," Bumgarner said. "I got it in there. I didn't think he'd be able to keep it fair but he did. That's what ultimately what cost us the game.
Overall, Bumgarner was pleased with his performance, just not the final result.
"I feel good about today, with the exception of that one pitch that really hurt me," he said.
Beltran has three homers in his last seven games.
"It was just a good hitter looking for a pitch and he got it," Giants manager Bruce Bochy said.
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Wainwright and Beltran helped St. Louis get back on track Thursday. The Cardinals, who have won seven of 10, lost 15-0 to the Giants on Wednesday, their worst home shutout defeat since 1961.
Wainwright (10-10) keyed the bounce-back effort allowing just five hits and one run over seven innings. He struck out seven, walked three and has given up two earned runs or less in each of his last five starts.
"We needed this win today," he said. "This is kind of what I live for. If there is a challenge out there, I'm ready for it. Not that you need more motivation but [the 15-0 loss] allowed me to focus a little bit more."
Jason Motte pitched the ninth for his 25th save in 29 chances.
Beltran, who leads the NL with 80 RBI, gave Wainwright all the necessary support with a 409-foot drive over the wall in left.
St. Louis manager Mike Matheny told his players to put Wednesday's loss behind them as soon as possible.
Beltran, who has eight first-inning homers, took those words to heart.
"Being able to go out there and score early, it was great," Beltran said. "That's what we needed to do. Yesterday was tough but we were able to bounce back."
Matheny felt Beltran's early home run served to set the tone for the afternoon.
"To get that bad taste out of your mouth is huge," he said. "When we strike first, we've got a real good chance of making something happen."
Jon Jay went 2 for 3 and reached base three times for St. Louis, which completed a seven-game homestand with a 5-2 mark.
Bumgarner retired the next five hitters following the Beltran homer. He also retired eight in a row between the third and fifth innings.
"For the most part, I followed the game plan," Bumgarner said. "And it worked except for a pitch or two."
San Francisco closed to 2-1 in the fifth on a bases-loaded sacrifice fly by Marco Scutaro.
Joaquin Arias and Bumgarner singled with one out before Wainwright walked Angel Pagan. Scutaro, who hit a grand slam and drove in a career-high seven runs Wednesday night, has hit safely in 11 of 13 games since he was acquired from Colorado on July 27. Wainwright then got Melky Cabrera to pop out to end the inning.
St. Louis pushed the lead to 3-1 in the sixth when Jay doubled, stole third and came home on Allen Craig's sacrifice fly.
Giants star Buster Posey extended his season-best hitting streak to 13 games with a single in the sixth.
San Francisco completed a seven-game road trip with a 5-2 record and a split of the four-game series in St. Louis. The teams are each 61-51 after play Thursday.
"We had some pretty good at-bats, but today we couldn't get a timely hit," Bochy said. "But, overall it was a very good road trip."
- Scutaro drove in 12 runs on the trip.
- The Giants had scored in the first inning in each of their previous seven road games before Wainwright stopped them.
- San Francisco has scored 93 runs in 13 games since the All-Star break.
- St. Louis opens a three-game series at Philadelphia on Friday. Kyle Lohse (12-2, 2.79 ERA) will face Roy Halladay (5-6, 4.02).
- The Giants begin a three-game set at home against Colorado. Tim Lincecum (6-11, 5.43) takes on Tyler Chatwood (1-2, 6.61).