Second-base umpire Mike Estabrook called pinch-runner Kyle Kendrick out on a pickoff even though shortstop Jean Segura tagged him without the ball and the Brewers held on to beat Philadelphia 4-3 on Saturday.
Kendrick was the second out of the inning, and the next batter doubled before Rodriguez was able to nail down his third straight save.
After the game, crew chief Tom Hallion told a pool reporter that it was an incorrect call after looking at replay.
"The ball goes in the glove and comes out of the glove with Kendrick diving back in and with Segura diving back for the ball," Hallion told a pool reporter. "Obviously, Mike was in the right position to make a pickoff play call like that. But the way that the play developed, the ball comes free and rolls right in Segura's bare hand and he comes up shows him the ball."
Before the ninth, Jonathan Lucroy homered and Wily Peralta tossed seven strong innings for Milwaukee.
After Rodriguez intentionally walked Domonic Brown, he retired Michael Martinez on a groundout to end the game. Kendrick went right to the video room after the play and said he was "just mad" when he saw the replay.
"He was in a bad position to see that, but that was the game," Kendrick said. "I score right there and we have a tie game and anything can happen."
Logan Schafer went 3-for-4 with a pair of doubles and an RBI for Milwaukee, which won its second straight after finishing May tied for the worst winning percentage (.214) in club history.
"We got some breaks again today," Milwaukee manager Ron Roenicke said. "This game is fun because you're always trying to figure it out. It's frustrating because you can't do anything about it. It really isn't fair."
Peralta (4-6) entered on a four-game losing streak but had one of his best outings of the season, surrendering two runs and eight hits with six strikeouts and a walk. Peralta successfully pitched out of trouble throughout and stranded runners at second in four of his seven innings, including when he struck out Brown with his final pitch in the seventh.
Brown had 12 homers in May with six in his last five games. He went 1-for-4 with a single and a pair of strikeouts Saturday. Freddy Galvis homered and Hernandez went 3-for-5 with a double for Philadelphia, which lost its third straight and fifth in seven games. The Phillies dropped to 8-24 when scoring three runs or less.
Galvis homered to lead off the ninth before Jimmy Rollins, who didn't start due to a sore foot, followed with a pinch-hit single. Kendrick ran for Rollins and went to second on Ben Revere's sacrifice bunt, but was picked off.
"It's unfortunate, but it's one of those plays that if any one of us - any umpire - had seen the loose ball, we certainly would have come in and helped Mike out with that," Hallion said. "The problem was that I don't think anybody saw the ball. I don't think anyone from the Phillies dugout or the Brewers dugout or Kendrick knew that the ball was on the ground."
After the Kendrick out, Rodriguez intentionally walked Brown to put runners on first and second with two outs before getting Michael Martinez to ground out to end the game.
"It's kind of how things have been going for us," Phillies manager Charlie Manuel said.
Tyler Cloyd (1-2) gave up three runs (two earned) on eight hits with three strikeouts and one walk in seven innings.
Delmon Young was responsible for two of the Brewers' first three runs, as his throwing error in the second inning allowed Lucroy to score after Schafer's RBI single that also scored Aramis Ramirez and gave Milwaukee a 2-0 lead.
Kevin Frandsen's RBI groundout in the fourth pulled the Phillies within 2-1. But the Brewers got the run back in the fifth when Segura tripled for a 3-1 lead.
Philadelphia closed within 3-2 on Erik Kratz's RBI single in the sixth, but Lucroy homered to left with two outs in the eighth off reliever Mike Adams. It was the third homer in two games for Lucroy, who went 5-for-5 with two homers and a double in Friday's 8-5 win over Philadelphia.
Notes: Schafer was filling in for regular center fielder Carlos Gomez, who got the day off. . Brown became the first player in Major League history with at least 10 homers and no walks in a month. . Brewers right-hander Mike Fiers (1-3, 5.66) is scheduled to face Phillies lefty Cliff Lee (6-2, 2.34) in the finale of the three-game series at 1:35 Sunday.