Bote, who made the last out in the 10th, started the inning on second base as mandated by Major League Baseball's extra-inning rule for the pandemic-shortened season. He advanced to third on a deep fly to right by Anthony Rizzo and jogged home on Baez's first career game-ending hit against Cody Ponce (0-1).
"It's definitely different," Bote said of the new rule. "With this season we're in this year, it definitely makes sense. But if you were playing a World Series game, you wouldn't want it decided like that."
Jeremy Jeffress (1-0) worked a scoreless 11th for the win.
The game was delayed 64 minutes by rain before the bottom of the ninth.
Chicago has won 10 straight games against Pittsburgh at Wrigley Field. The Cubs outscored the Pirates 81-31 in the previous nine games, hitting 24 homers during that span.
In both the 10th and 11th, the Pittsburgh runner on second base to start the inning made a baserunning out. In the 10th, catcher Jacob Stallings tried to score from second on a single by Josh Bell with no outs and was thrown out by left fielder Kyle Schwarber. In the 11th, Kevin Newman was thrown out at third trying to advance on a grounder to shortstop.
The Pirates had outfielder Gregory Polanco on the bench and manager Derek Shelton was asked if he considered running for Stallings in the 10th.
"I didn't think that was a very good opportunity to put GP in the game," Shelton said. "It was a wet track, he had been sitting for a while and with his record of previous injuries I didn't feel it was a good time for him to be on the field."
The Pirates took a 1-0 lead in the first on Newman's first homer of the season.
After being held without a baserunner in the first four innings, the Cubs tied it at 1 in the fifth. Willson Contreras led off with a double and Schwarber followed with a liner off the wall in center for an RBI double.
Cubs starter Jon Lester allowed four hits in six innings.
Pirates starter Steven Brault retired all nine batters he faced in three innings, striking out four.
"That's a lot of innings we asked out of our bullpen tonight," Cubs manager David Ross said. "Great job by the bullpen."
BRYANT OUT AGAIN
Chicago star Kris Bryant was out of the lineup for a second straight game, a day after reporting a stomach ailment. Bryant was tested for the coronavirus on Friday and Saturday, and the Cubs said both tests were negative. He is scheduled to be tested again on Monday.
Ross said Bryant was feeling better Sunday and the team will follow the MLB protocols.
"He really needs to be commended for going in and getting checked out," Ross said.
Pittsburgh acquired right-hander Tyler Bashlor from the New York Mets before the game in exchange for cash considerations. The 27-year-old Bashlor was designated for assignment July 28. To make room on the roster, left-hander Robbie Erlin was designated for assignment.
Pirates: RHPs Mitch Keller and Michael Feliz were placed on the 10-day injured list before the game after each had to leave Saturday's 4-3 loss because of injury. Keller started and left in the third with left side discomfort. Feliz departed in the eighth with right forearm discomfort. Ponce and LHP Sam Howard (two scoreless innings) were activated from the taxi squad and saw immediate action.
Cubs: RHP James Norwood (shoulder) was placed on the 10-day IL, and LHP Justin Steele was recalled from the team's camp in South Bend, Indiana.
Pirates: Lefty Derek Holland (0-0, 3.18 ERA) takes the mound Monday night in the opener of a two-game series at Minnesota.
Cubs: Righty Alec Mills (1-0) makes his second start of the season in the opener of a two-game series against Kansas City at Wrigley on Monday night.
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