Junior Spivey mishandled Luis Rodriguez's grounder for an error with the bases loaded in the 11th inning and Stewart hit a tying two-run homer in the ninth as the Twins rallied for a 6-5 victory over the Brewers on Sunday.
Rodriguez then hit a hard grounder, and with the infield playing in, second baseman Spivey bobbled the ball and could not recover in time to make a play.
"Over the past few years, we've shown we can play to the last out," Cuddyer said. "This was the first time this year we really looked down and came back."
The Twins were 0-15 when trailing after eight innings this season.
Jesse Crain (3-0) pitched a scoreless 11th inning for the victory.
The game started as a pitchers' duel between the Brewers' Wes Obermueller and the Twins' Santana, who didn't allow a hit until there were two outs in the sixth inning. It came down to the two best bullpens in baseball. Twins relievers had a major league-best 2.40 ERA, and Milwaukee's pen was an NL-best 2.81.
Neither bullpen was effective as the teams scored eight runs over the final four innings.
"That's where the tide turned right there," Brewers manager Ned Yost said.
Ford followed with an RBI double. Turnbow got the next two batters, but Stewart hit a fastball just over the right-field fence to tie it at 5. The homer came on Turnbow's 40th pitch and resulted in his second blown save in eight appearances.
"I just need to get that third out," Turnbow said. "I was trying to go away and [Stewart] got a hold of it. It happens."
Brady Clark homered off Santana with two outs in the sixth inning for Milwaukee's first hit, and the Brewers took a 2-1 lead in the seventh on Wes Helms' RBI single. The Brewers added two more runs in the eighth off reliever Juan Rincon and one in the ninth off closer Joe Nathan.
The Twins closed to 4-2 in the eighth when Turnbow threw a wild pitch that scored Stewart, who had singled off Ricky Bottalico.
Stewart's homer prevented Santana from losing consecutive starts for the first time since May 18-June 3 of last season, when he lost four in a row. The AL Cy Young Award winner struck out 11 to increase his major league-leading total to 83.
"As you can see today, it takes more than one guy to win a game," Santana said.
Obermueller gave up three hits and one run in six innings for the Brewers. He walked three and struck out two.
Santana was dominant through the first five innings, striking out nine. Jeff Cirillo was the only Brewers player who did not fan in that period.
When Santana struck out Chad Moeller for the second out of the sixth inning, he had his 18th career double-digit strikeout game. But Clark followed with a homer on an 0-1 slider, tying the score at 1.
In the seventh, Spivey had a one-out double down the left field line; an out later, Helms hit a 3-2 pitch off third baseman Cuddyer's glove to put the Brewers up 2-1.
Milwaukee added two more runs in the eighth on a throwing error by Torii Hunter and Bill Hall's infield single. The Brewers made it 5-2 when Nathan walked Geoff Jenkins with the bases loaded in the ninth.
Rodriguez got his first major-league hit with a single in the ninth inning. ... Twins pitchers had 17 strikeouts, tying a club record set in 1966 and matched in 1987. ... Brewers reliever Julio Santana got off to a wild start in the seventh inning, throwing the first pitch over the head of leadoff hitter Hunter and just missing him on the second pitch. He ended up walking Hunter on four pitches but got out of the inning. ... The teams drew 90,645 over the three-game series.