
Metz striker Georges Mikautadze made no mistake from the penalty spot in the 23rd minute as he scored his 11th goal across all competitions this season after Lille were penalised for handball.
Eight minutes later, Lille left-back Ismaily equalised with a shot into the bottom corner following an assist by Jonathan David and Yusuf Yazici put the visitors ahead just before half-time with a right-foot strike.
Lille, who dominated possession throughout, have won four of their last five Ligue 1 matches with the loss coming against top-three rivals AS Monaco.
Lille moved up to third in the standings on 55 points, three behind second-placed Monaco who have a match in hand and visit Olympique Lyonnais later on Sunday. Metz are 16th on 29 points with three matches left.