Bautista will move from right field to third base once the team has finished its current National League road trip, in order to open up a spot for Thames, who will join the team on Friday, in the outfield.
"It's not going to be two games at third, two games in the outfield. It's going to be every game at third," general manager Alex Anthopoulos said of Bautista. "He will be entrenched as the guy at third base going forward for us."
Third base has been Toronto's least productive position this season, with Blue Jays third basemen hitting just .177 (47-for-266) in 75 games.
Bautista played 48 games for the Blue Jays at third in 2010, hitting .281 with 17 home runs and 40 RBIs while playing the position. He was thought to be the team's third baseman to start 2011 until Edwin Encarnacion claimed the spot in Spring Training, allowing Bautista to return to the outfield.
Since then, Encarnacion has been relegated to a role as a bench player, while Jayson Nix has made the majority of the starts at third, with John McDonald and Mike McCoy spelling him.
Nix has hit just .136 (12-for-88) in 27 games since returning from the 15-day disabled list on May 18 with a .181 on-base percentage. He now joins Encarnacion on the bench as Bautista makes the majority of the starts at third base going forward.
The Blue Jays have struggled offensively throughout the first six games of their current 10-game, four-city road trip. The team has collectively hit .168 and scored just 10 runs over that span and has been outhit in five of the six contests.
Anthopoulos said he explored the trade market "at length" for a solution at third, but he wasn't able to find a deal to his liking. That meant the GM had to find a spark for his slumping lineup internally.
For his part, Bautista told his general manager he has no problem moving from the outfield back to the infield.
"We know he's always on board. We could ask Jose to stand on his head, and if it's going to help the team, he's going to do it," Anthopoulos said.
Thames will see plenty of action soon as Toronto continues to look for an offensive catalyst in the lineup.
"Thames is really swinging a hot bat down in Las Vegas. He's done a good job," Anthopoulos said. "Thames is going to be getting a lot of at-bats."
Thames will likely get a start in the outfield for Corey Patterson or Rajai Davis during the St. Louis series. Bautista -- currently leading the Majors in home runs -- will remain in right for the next few days as he takes grounds balls at third and gets used to the position again. By the time the Blue Jays open a three-game set with the Pirates in Toronto on Tuesday, the plan is to have Thames in the outfield and Bautista at third base permanently.
The delayed arrival of top prospect Brett Lawrie, who continues to recover from a non-displaced fracture in his hand after being hit by a pitch earlier this month, was also a factor in this move.
Lawrie -- who would likely be with the Blue Jays right now had he not been injured -- is still having trouble gripping a bat and will likely not see the field again until August.
"He's taken a little longer to heal than we had hoped," Anthopoulos said. "We still envision him as being the long-term guy at third base, but you just don't know with an injury how long that's going to take."
The 21-year-old Lawrie was on a tear prior to being injured, hitting .354 with 15 homers and 49 RBIs in 52 games with Las Vegas.
"The progression is probably going to take a little bit longer than we had initially hoped," Anthopoulos said of Lawrie's recovery. "Ultimately, if things develop, whether it's Brett coming back to action or something else develops, we know Jose can go back to the outfield."
Lawrie's unfortunate injury, of course, is good fortune for Thames who will likely be with the Blue Jays long term, splitting time between left field, right field and designated hitter.
The 24-year-old began the season with Triple-A Las Vegas, where he hit .342 with six home runs and 30 RBIs in 36 games.
Those numbers earned him a callup to the big league club for a brief stint in May, when he hit .286 (12-for-42) with a pair of doubles and four RBIs in 13 games. He went 3-for-5 in his final game with the team June 1 before being sent back down to Triple-A.
The time in the big leagues clearly had a profound effect on Thames, who set the Pacific Coast League on fire after returning to Las Vegas, batting .375 (24-for-64) with eight doubles, two triples, one home run and 15 RBIs.
McCoy was optioned to Triple-A to make room for Thames on the big league roster.
Arden Zwelling is an associate reporter for MLB.com This story was not subject to the approval of Major League Baseball or its clubs.