The 28-year-old registered his tenth goal of the season to steer Gus Poyet’s men to their 14th league win.
Following their loss to Paris Saint-Germain in their last game, the Girondins’ aim of a good start was frustrated with Remy Cabella’s 28th-minute strike from the penalty spot.
However, the Matmut Atlantique outfit swiftly responded two minutes later with Sankhare levelling proceedings after an assist from Youssouf Sabaly.
And in the 36th minute, Jules Kounde fired home to give the visitors the lead.
With one minute left of regular time, Jean-Louis Gasset’s side got a chance to equalise from the penalty spot but Cabella failed to convert.
They were soon punished for the missed chance with Malcolm sealing the victory for the Navy and Whites at the death.
With the win, Bordeaux are now eighth in the table with 49 points from 36 matches and they clash with Toulouse in their next league game on May 12.