A woeful error from Shillong Lajong goalkeeper T P Rehenesh gave Sporting the lead, but Uilliams Souza Silva secured the equaliser for the home side just four minutes later with a free kick.
However, striker Odafa Okolie delivered the winner for Sporting de Clube in the 83rd minute.
The victory took the Goan outfit to 20 points, up to sixth position from a lowly 10th. They have now won four of their last five games.
However, four minutes later, Uilliams found the equaliser with a dipping free kick that caught Sporting's keeper Ravi Kumar off guard, the ball bouncing over the diving keeper.
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Odafa then benefited from a defensive lapse from an otherwise alert Lajong. The Nigerian was completely unmarked on the right flank and a pass to the striker allowed him the perfect chance to score a goal.
The two clubs appeared to adopt differing strategies during the 90 minutes of action, with Lajong pushing several men up front, while the visitors seemed more content to hang back, with only Odafa really pressing in attack.