An early goal from Lucas Ocampos was cancelled out by Firmin Mubele in the first half only for Greek international Mitroglou to secure all three points for the visitors two minutes after he had come onto the pitch.
The result left third-placed Marseille on 59 points from 29 games, four points adrift of second-placed Monaco, who beat Strasbourg 3-1 away on Friday. Paris Saint Germain are runaway leaders on 77 points.
Olympique Lyonnais are fourth on 54 points after beating Caen 1-0 at home earlier on Sunday with a second-half goal by Bertrand Traore.
In Toulouse, Marseille got off to a fine start when Ocampos tapped in after a free kick was deflected into his path by Luiz Gustavo.
The hosts equalised nine minutes later, Mubele beating Steve Mandanda from point-blank range from Issiaga Sylla's cross.
But OM increased the pressure after the break and were rewarded when Mitroglou volleyed home in the 79th minute after replacing fellow striker Valere Germain.
Bouna Sarr and Mitroglou both hit the woodward for Marseille in stoppage time but their near misses had no consequence with Toulouse failing to offer a threat in the dying seconds.
(Reporting by Julien Pretot; Editing by Ian Chadband)
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