Encarnacion left Thursday's game against the Red Sox in the top of the fourth inning as a precaution after experiencing soreness in his left knee. He was originally considered day-to-day.
The third baseman was not in the Jays' lineup for any of the club's three games against the Angels over the weekend, and was placed on the 15-day disabled list with a left hamstring strain on Monday. The move is retroactive to Friday.
Encarnacion was acquired from Cincinnati, along with reliever Josh Roenicke and pitching prospect Zachary Stewart, at the July 31 Trade Deadline in exchange for third baseman Scott Rolen. Encarnacion is hitting .202 with six home runs and 19 RBIs in 59 games this season.
When Encarnacion left Thursday's game, he was replaced by utility infielder John McDonald. Jose Bautista has been starting at third base since then, but Blue Jays manager Cito Gaston said Bautista would not be the only one filling in at third while Encarnacion is unavailable.
"He won't be there every day," Gaston said. "That's something I have to think about."
Bautista and Encarnacion are the only players on the club's Major League roster who have spent time at third base this year.
Downs, who is 1-3 with a 3.41 ERA and nine saves in 35 games this year, is returning from his second trip to the DL of the season due to a toe injury. He originally sprained the big toe on his left foot while running out of the batter's box in an Interleague game in Philadelphia.
He was placed on the 15-day disabled list and was activated three weeks later, but struggled in his return and found himself back on the DL on Aug. 2 when the injury persisted.
Downs took over as the team's closer when B.J. Ryan -- who was released in early July -- got off to a poor start to the season.
Gaston said on Sunday that Downs would likely not be the closer right away upon his return. Instead, Downs will ease back into the team's bullpen and may take over ninth-inning duties again, depending on how he performs in his return.
Right-hander Jason Frasor has been filling in as the stopper in Downs' absence.
Erika Gilbert is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.