"It's a game of inches and that ball could've hooked foul," Astros interim manager Tom Lawless said. "They did enough to score two in the ninth and you can't blame anybody. We played hard and we pitched well and they just happened to get good wood on the ball and hit a home run."
The Astros enter the final game of the season with a 70-91 record and needing a win to give them a 20-game improvement from last year's 51-loss season.
But much of the focus for the Astros will be on All-Star second baseman Jose Altuve, who went 0-for-4 on Saturday and holds a slim three-point lead over Victor Martinez for the batting title. Altuve is hitting .340, and Martinez is at .337.
"We'll see what happens," Lawless said. "It should be fun."
Sipp, who threw two scoreless innings on Friday, entered the ninth with a 1-0 lead in an attempt to polish off a two-hit shutout. Eric Young Jr. tripled with one out, and he was still at third when Duda came to the plate with two outs and delivered.
"I was just trying to make contact," Duda said. "Obviously, I haven't hit lefties all too well this year, that's pretty obvious. But I'll get better at it. In the past I've hit lefties a little better than I have this year. A work in progress still."
Sipp (4-3) left a 1-0 fastball over the plate.
"I knew if I made good pitches that I matched up against him," he said. "I made one mistake and he took advantage of it, and a guy with that much power, you've got to locate at least down and I left it up. He did what most power hitters do with fastballs that are elevated in the middle, and I've got to do a better job of locating."
Astros catcher Jason Castro, making his final start of the season, ripped an RBI double into the right-field corner in the sixth inning to score Dexter Fowler from first base and give Houston a 1-0 lead.
The Astros have scored nine runs in their past five games and were 1-for-7 with runners in scoring position Saturday.
"We're trying to get some runs," Lawless said. We had first and third [in the sixth] and would have scored some runs if we could get a ball in the outfield, and we couldn't do it again tonight. We tried to hold a one-run lead and in Major League Baseball that's kind of hard because they have some good hitters on the other side. It's a tough one."
Samuel Deduno, a late-season waiver claim making his first start with the Astros, threw four scoreless innings -- he was on a pitch limit -- and struck out four batters. He also shot a double to left field in the third for his first Major League hit and the first hit by an Astros pitcher this year.
Twins starter Rafael Montero held the Astros to one run and six hits in 5 1/3 innings.