Beltran strained his left knee running out a double-play ball in the first innings and the Cardinals said he was day to day.
Kyle Lohse worked around a season-worst five walks in 5 2-3 innings. Mitchell Boggs struck out Hunter Pence and Brandon Belt with two on to end the seventh. Jason Motte earned the first two-inning save of his career to reward what remained of a sellout crowd of 45,850 perhaps a third that stuck around for a game that lasted 3 hours, 2 minutes, about a half-hour shorter than the delay.
"They said if we didn't score I was going to go out there. I was in the clubhouse running around, I've never really had to sit around like that," Motte said. "It was probably the most nervous I've ever been."
Giants second baseman Marco Scutaro had two hits and a clean game in the field, two days after Matt Holliday rammed him breaking up a double-play ball. Manager Bruce Bochy had said there would be no retaliation, and Game 3 was collision-free.
The big winners in a delay that featured about a half-hour without rain while officials awaited a second, smaller front: Beer vendors, by a single out. Alcohol sales are cut off after the seventh inning in all stadiums.
Cain lost for the second time this postseason, giving up three runs on five hits in 6 1-3 innings. The Giants, who entered the game batting just .217 in the postseason, were 0 for 7 with runners in scoring position.
The Cardinals snapped the Giants' five-game road winning streak in the postseason, three of them this year. Game 4 is in St. Louis on Thursday night, with Adam Wainwright pitching for the Cardinals. Tim Lincecum will start for the Giants.
"He's a guy we want out there. He's been throwing the ball well," Bochy said. "We've got to bounce back."
Carpenter followed Jon Jay's two-out single with a homer off Cain in his first at-bat of the NLCS.
Beltran is batting .400 in the postseason with three homers and six RBIs, but Carpenter had big numbers against Cain. He was 4 for 4 for his career against Cain, all four of the regular-season hits for singles.
"He's a really good pitcher obviously," Carpenter. I've had some success. I just go up there and try to battle, get a good pitch to hit."
This one was a much bigger deal, a drive on a 2-2 count that soared over the Cardinals bullpen in right field and was estimated at 421 feet.
Carpenter entered the game 1 for 5 in the postseason, all five pinch-hit appearances. He had an RBI single in the wild-card playoff against Atlanta. He got 14 of his 46 RBIs in April as the primary sub at first base for injured Lance Berkman.
On Tuesday, Carpenter was among a group of seldom-used hitters trying to stay sharp by facing Jake Westbrook in a simulated game. The rest of the team had the day off.
Umpires called for the tarpaulin right after the Cardinals made it 3-1 on a run-scoring single by Shane Robinson and Cain was lifted.
It was the third game delayed by rain this postseason and a fourth, Game 4 of the Yankees-Tigers ALCS, was postponed later Wednesday night. Two games between the Yankees and Orioles in Baltimore began late because of inclement weather.
The rain intensified less than 10 minutes after the field was covered, chasing most fans who had remained in their seats up to that point. Spotters for the National Weather Service reported 60 mph winds in nearby St. Charles County.
A highlight of the delay was a Pac-Man style chase. Ushers pursued and finally apprehended a fan who jumped out of the stands to get a baseball near the warning track in left field, and then jutted in and out of aisles to elude several ushers who had been closing in.
The storm had been widely anticipated. Some forecasts called for a 70 percent chance of rain. Both managers fielded questions Tuesday and Wednesday about whether the probability of precipitation would affect their selection of the starting pitcher.
Both said they couldn't worry about the weather, and the starters combined for 208 pitches.
"I've been caught before where you try to predict what's going to happen with the rain and started," Bochy said. "Just a couple years ago I started a pitcher thinking the same thing and it didn't rain for four or five innings. Then I put my starter in and then it started raining, and so it came back to bite me."
Lohse is 2-1 with a 1.96 ERA this postseason despite uncustomary control woes. He was among the majors' best control pitchers this season, averaging 1.62 walks per nine innings.
The Giants entered 70-22 when scoring first, including the postseason, and took the lead in the third on Pablo Sandoval's run-scoring groundout after leadoff hits by Angel Pagan and Scutaro, whose legs looked just fine on an opposite-field double flared just over first baseman Allen Craig's glove.
Beltran leads all players with eight extra-base hits in the 2012 playoffs and is a career .375 hitter in the postseason, highest ever among players with a minimum of 100 at-bats.
NOTES: Danny Cox, who pitched for Cardinals World Series teams in 1985 and 1987, threw a perfect strike on the first pitch. ... According to STATS LLC, Lohse walked two batters in the same inning four times in 2012. ... Jay, who was hit by a pitch to start the game, was plunked 15 times in the regular season. ... Matheny had 122 lineups during the regular season but has stuck with the same eight throughout the postseason. ... The Cardinals are 9-2 in Game 3 of the NLCS, the lone losses coming in 2004 and '05 at Houston. This win ended a streak of scoring at least six runs in the last eight postseason victories dating to Game 3 of the World Series last year, the longest streak of its kind in postseason history. St. Louis entered averaging 7.6 runs in 16 wins the last two postseasons and just 2.3 runs in the 10 losses. ... The Cardinals have played in eight best-of-seven series in which they were tied 1-1 and played Game 3 at home, and have won all of them. They won six of the previous seven series, according to STATS LLC
P San Francisco at St. Louis
Thursday, 6 p.m., Ch. 13