The two-time home run champion took off his helmet and acknowledged both the crowd and the Blue Jays' dugout as fans rose for a prolonged ovation. Bautista drew a five-pitch walk and then scored when Asdrubal Cabrera followed with a home run.
Before the game, Bautista also received an ovation at the end of a video tribute featuring highlights of his 10 seasons with the Blue Jays, including back-to-back American League Championship Series appearances, in 2015 and 2016.
Bautista was playing his first game in Toronto as a visitor since June 24, 2004, according to ESPN Stats & Information research. He went 1-for-2 with three walks and a run scored in New York's 8-6 loss.
"Great to be recognized, great to acknowledge the fans and great to know they feel good I'm back and wanted to recognize me,'' Bautista said.
The Blue Jays played Bautista's old walk-up music, Usher's "OMG,'' before his first at-bat.
"That caught me by surprise,'' he said.
The six-time All-Star exchanged warm embraces with several former Blue Jays teammates during batting practice and signed autographs for fans alongside New York's first base dugout. Fans in right field rose to applaud Bautista as he took his position in the bottom of the first.
Bautista played 12 games for the Atlanta Braves in May and joined the Mets on May 22. He's batting .250 with three homers and 13 RBIs in 36 games with New York.
The Associated Press contributed to this report.