That trade didn't get the expected results for Toronto, and general manager Alex Anthopoulos is moving the team in a different direction.
Bonifacio was traded by the Blue Jays on Wednesday to the Kansas City Royals for a player to be named later or cash, while Johnson will have an MRI to see how long it will take for him to recover from a strained right forearm.
"Clearly they haven't played and performed the way we expected them to when we acquired them, there's no doubt about that at all," said Anthopoulos when asked if he was second guessing the Marlins deal. "But the process when you go into these things you know there's no guarantees of performance.
"Sometimes you have guys that perform a lot better than you thought they could both internally and externally."
Bonifacio hit .218 as a utility player this season with three home runs, 20 runs batted in and 12 stolen bases. He saw time at second base, shortstop and all three outfield positions. Kansas City claimed the 28-year-old on waivers, forcing Anthopoulos to strike a deal.
"It just didn't work out," said Blue Jays manager John Gibbons. "Ton of talent, got some opportunities. It just never came together on a consistent basis. We loved the guy, what he brings to the park. He shows up to play, he could make some things happen, there just wasn't enough consistency there."
The Toronto front office agreed with Gibbons' assessment after the trade with the Royals was complete.
"I think we expected him to be a better player, a better player overall," said Anthopoulos. "I think there's no doubt about that, we thought we'd get more out of him offensively, defensively, all of it.
"That didn't happen. I don't want to diminish his talent or take away his work ethic."
Johnson (2-6) has struggled on the mound all season with a 6.20 earned-run average. The right-hander was placed on the 15-day disabled list on Aug. 7 with a strained right forearm. An MRI scheduled for Wednesday night will decide if he plays for Toronto again this season.
"It's too hard to tell," said Anthopoulos. "I think we'll know more tonight and certainly tomorrow and then I'll be able to make a determination."
The Royals are 6 1/2 games out of first place in the American League Central and four games back of the second wild-card spot.
Trading Bonifacio cleared space on the roster for outfielder Kevin Pillar, who was recalled from Buffalo. Pillar, the Blue Jays' 32nd-round pick in the 2011 draft, could make his major-league debut at Rogers Centre on Wednesday night against the Boston Red Sox.
"This gives us a chance to bring Pillar up and get a look at him too," said Gibbons.
Gibbons said that Kawasaki's return to Toronto already had an impact on the Blue Jays' clubhouse.
"When he walked into the clubhouse you could hear that the noise level rose," said Gibbons.
More changes could be in store soon for the last-place Blue Jays, who are 17 games back of the American League East-leading Red Sox.
Johnson and Bonifacio are not the only pieces of the Miami trade that have had issues. Although Reyes had a hot start to the season, he missed two and a half months with a severely sprained left ankle.