The team made the announcement Thursday with training camp set to open on the weekend at Bishop's University.
Despite suffering a season-ending knee injury last September, Whitaker led the team in all-purpose yards with 1,225 in just 10 starts. He racked up 631 rushing yards on 123 carries with four rushing touchdowns.
The 27-year-old also became a favourite target for veteran quarterback Anthony Calvillo out of the backfield, amassing 49 receptions for 516 yards and five touchdowns through Week 12.
Whitaker tore the ACL in his right knee in a 28-17 win over Saskatchewan on Sept. 16 and missed the final two months of the season.
"We welcome Brandon back with open arms. We are as much interested in the well being of Brandon's health as much as him returning to the playing field," Alouettes' general manager Jim Popp said in a statement.
"Approximately a week to 10 days ago Brandon was evaluated thoroughly by our medical staff and also did a voluntary workout for our Head Therapist Rodney Sassi. He was impressive and showed that he is determined to return to the playing field and stay an Alouette."
In 2011, Whitaker led the league in rushing yards with 1,381 on his way to earning his first CFL and East Division all-star nominations.
Whitaker is going into his fifth season with the Als and has two Grey Cup titles with the team (2009 and 2010).