Polanco had played in two straight games after missing a week because of an ailing left wrist.
The 36-year-old has a small tear in his tendon, a situation that required him to get a cortisone shot last week, and Manuel will be cautious as a result.
"We got in at four o'clock in the morning, and Polanco has been banged up, and I figured that, especially when I found out [the Blue Jays have] two lefties going Saturday and Sunday, I would keep him back," Manuel said. "That's how I wanted to use him."
Polanco, a right-handed hitter, will face left-handers Ricky Romero and Brett Cecil on Saturday and Sunday, respectively.
A 15-year veteran, Polanco is batting .280 on the season with a .668 OPS.
Mike Fontenot got the start at third base on Friday, batting eighth.