Toronto's Kyle Lowry forced the extra period by hitting a 3-pointer with 12 seconds to go in the fourth period, but the Bobcats never trailed in overtime on their way to a second straight win.
Even though the Raptors could not score for the first 3:42 of the extra session, they had a chance to take the lead when DeMar DeRozan went to the line in the final seconds with his team trailing by only one.
DeRozan could hit just 1-of-2, however, and a second overtime was looming until Walker made his buzzer-beating shot.
Walker scored 29 points and Al Jefferson added 24 points and 11 rebounds for the Bobcats.
Toronto, which had won two straight, was led by DeRozan with 30 points.