The Toronto Blue Jays announced the upcoming operation on Twitter today.
They say Bautista is expected to be back for spring training.
Bautista is ninth in the American League with 27 home runs this season, despite missing six weeks of play in July and August with inflammation in his wrist.
He left Toronto's 8-2 loss to the Baltimore Orioles on Aug. 25 with discomfort in his left wrist.
He was placed on the 15-day disabled list the next day.