Malcolm fired home with his left foot after meeting a ball into the box from Francois Kamano to maintain his side's unbeaten start to the new season.
Bordeaux went into the game on the back of a goalless draw at Lille while south-west neighbours Toulouse also drew 0-0 at Troyes.
But it was the home side who started much better with Corentin Jean shooting straight at Benoit Costil, while Andy Delort also flashed a header wide.
Costil saved brilliantly to deny Delort and Ola Toivonen also came close as the visitors struggled to stay on level terms.
But a single defensive lapse by Toulouse allowed Malcom to pounce, hitting a powerful effort in off the crossbar to take the points in style.