Johnson, who was hitting .289 with three doubles and three RBIs, had spent his entire career with the Blue Jays.
"I don't have any hard feelings," Johnson said. "I don't have much of a choice right now except to move on. It's really all I can say."
The 31-year-old was drafted in the 17th round (523rd overall) in 1998 and was signed by Toronto through the end of this season.
Johnson had a breakout year in 2006, batting .319. But a herniated disk problem put him on the disabled list last season, when he hit just .238 in 79 games.
"I don't think he will have any trouble finding a job," general manager J.P. Ricciardi said. "He could go someplace and play more than he would have here."
Stewart began the day hitting .226 this spring since signing a minor league contract Feb. 24.
"It was tough," manager John Gibbons said. "We feel Stewart is going to give us more offense this year and we are going to need that."