Santana has not played since he underwent surgery to remove calcium deposits from his right middle finger in early February.
Santana, 35, had hoped to come back in late May, but suffered several setbacks after his surgery.
Santana had his last start on Friday for Triple-A Rochester, holding Norfolk to one run over six innings.
"It's going to be a little bit of changing it up in terms of where to slot [Santana] in," said Molitor. "We thought keeping him on regular rest would be good."
Adalberto Mejia will start the Blue Jays-Twins series opener on Monday and is expected to be optioned after the game. Molitor said that pitchers Kyle Gibson, Lance Lynn and Jake Odorizzi will make their next starts on extra rest with the addition of Santana.
Santana went 16-8 with a 3.28 ERA in 33 starts last season, striking out 167 and walking 63 in 211 1/3 innings.