The CFL club made the announcement Monday, adding the move was made prior to Sunday's 37-30 home loss to the Toronto Argonauts.
Whitaker missed the final half of last season with a knee injury and suffered a separated shoulder in late July against the Edmonton Eskimos.
The 27-year-old has rushed for 338 yards and two touchdowns on 66 carries so far in 2013. Whitaker's best season came in 2011 when he gained 1,381 yards and four TDs on 226 carries.
The Baylor University product also caught 72 passes for 638 yards and six touchdowns.
The 4-6 Alouettes say there is a chance that Whitaker will be removed from the nine-game injured list depending on his recovery process.