Walker, a Pittsburgh native, drove a 3-2 pitch from Carlos Villanueva (0-1) into the right field seats to send the largest crowd in PNC Park history home happy.
The blast made a winner of Bryan Morris (1-0), who worked around a one-out single in the top of the 10th with a pickoff that was overturned in Pittsburgh's favor on a replay challenge.
It was the second challenge of the game.
The first use of expanded replay in the majors occurred in the fifth inning when the Cubs put together the first threat of the game after Nate Schierholtz led off with a single and Darwin Barney drew a walk. Jeff Samardzija tried to bunt the runners over, but Francisco Liriano quickly fielded the ball in front of the mound, threw to third for the first out and Pedro Alvarez fired back to first for the double play.
Cubs manager Rick Renteria calmly and slowly walked toward first base umpire Bob Davidson to question the close call and decided he wanted to challenge it. The review, which took about two minutes, upheld Davidson's decision.
The Pirates are trying to build off a banner 2013 season. They earned a National League wild card berth last year for their first playoff appearance since 1992 and the fans packed the house on Monday with a PNC Park attendance record of 39,833. Andrew McCutchen, last year's NL MVP, went 1-for-3 and Travis Ishikawa added two hits.
Liriano, last year's NL Comeback Player of the Year, went the first six innings for Pittsburgh and surrendered four hits with three walks and 10 strikeouts.
Samardzija, who threw eight innings of two-hit shutout ball in Chicago's 3-1 win at Pittsburgh last year on Opening Day, yielded five hits in seven scoreless innings on Monday. He walked two and struck out three.
Bonifacio had four hits for the Cubs, who are coming off their fourth straight losing season at 66-96. Chicago had plenty of chances Monday, but finished a dismal 0-for-11 with runners in scoring position.
The Cubs threatened in the sixth when Junior Lake led off with a base hit to left and Starlin Castro walked. Liriano then fanned Anthony Rizzo and got Mike Olt on a pop up before striking out Welington Castillo to end the inning.
Pittsburgh had a great chance to score in the bottom of the sixth after Starling Marte led off with a double and McCutchen drew a one-out walk. Alvarez then ripped a pitch up the middle, but the Cubs had him played that way to start an easy double play.
Bonifacio began the top of the eighth with a double and became the first runner to reach third on a bunt, but he was caught in a rundown after Castro grounded to second and Rizzo popped up to keep the game scoreless.