Bautista's home run landed outside of the ballpark at Bright House Field. The game was called in the middle of the seventh inning.
"It felt pretty good, I can't deny that," Bautista said. "More importantly I felt like I was seeing the ball great. I haven't been playing for a while so that's a positive."
Bautista missed the last six weeks of the season with a hip injury, the second straight year in which he ended the season on the disabled list. He hit 28 home runs in 2013 after reaching 27 the year before.
He was 1 for 2 with a walk and two runs scored Wednesday.
Ryan Howard and Marlon Byrd each had run-scoring singles off former Phillies left-hander J.A. Happ in the bottom of the first.
Phillies: Hernandez, making his Phillies debut, allowed two runs on four hits in two innings. He is the front runner for the fifth starter's job after signing a one-year, $4.5 million contract as a free agent this winter.
"When I face him I try to throw changeups and sinkers down," Hernandez said of the home run to Bautista. "But today I got down in the count and had to throw it down the middle. I missed up."
Blue Jays: Happ struggled in his only inning against his former team. Although he ended up striking out the side, he gave up four hits and a walk in facing eight batters. Happ finished second in the NL Rookie of the Year voting in 2009, when he went 12-4 with a 2.93 ERA. Happ was 5-7 with a 4.56 ERA in 18 starts with the Blue Jays last season.
Philadelphia left-hander Cole Hamels threw off the mound for the first time this spring. The 30-year-old Hamels entered camp behind the rest of the pitchers after experiencing biceps soreness in November. Hamels will throw another side session on Saturday and isn't likely to pitch in a Grapefruit League game for another two weeks.
Howard got off to a fast start, singling in a run in the bottom of first. The Phillies' first baseman played only 80 games last year because of knee problems. Manager Ryne Sandberg is impressed with Howard's progress.
"I really like Howard's aggressiveness early in the count with men on base," Sandberg said.
Cliff Lee will make his first start of the spring on Thursday, when the Phillies take on the Blue Jays for the second straight day, this time in Dunedin. But several Phillies regulars will not be in the lineup, including Howard, Jimmy Rollins and Chase Utley.
Toronto is starting knuckleball pitcher R.A. Dickey. But Sandberg says he's not sitting his regulars because of Dickey's unusual pitch.
"I don't think that comes into play that much," Sandberg said. "If they keep it simple, it comes down to see the ball and hit it."