Manager John Farrell said the addition of McCoy -- who can also play in the outfield if needed -- gives the Blue Jays some middle infield depth. Second baseman Kelly Johnson is nursing a tender hamstring and shortstop Yunel Escobar has had a tight left groin over the last few days.
Thames, 25, had a strong spring and beat out Travis Snider for the starting job in left field. Thames posted solid numbers at the start of the season but struggled over the last few weeks.
In 46 games, he hit .243 with seven doubles, three home runs and 11 RBIs.
"We feel like it will be a short-term thing and he has a very real opportunity to get back here," Farrell said. "But the factors involved are really what drove this decision."
McCoy, 31, hit .238 and drove in 14 runs in 44 games with Las Vegas.
"For the time being, this is what we needed to cover ourselves," Farrell said.
Johnson and Escobar were listed first and second in the lineup for Tuesday night's game against the visiting Baltimore Orioles. McCoy was expected to be available off the bench.
Thames played in 95 games for Toronto last season. In 141 career games with the Blue Jays, he hit .257 with 31 doubles, 15 homers and 48 RBIs.
Snider, 24, is hitting .333 this season at Las Vegas but is currently on the disabled list with a wrist injury. Farrell said Snider is still receiving treatment and has yet to start a hitting program.