Forlan's goal came in the 51st minute -- a sweetly struck left-footed strike -- and proved decisive.
Malaga defender Diego Lugano gave Uruguay the lead from close range inside the opening 20 minutes, following a cross from Forlan, only for Chelsea midfielder John Obi Mikel to bring the Super Eagles level with a brilliantly taken goal shortly before half time.
Uruguay and Nigeria now each have three points in Group B, but it is Uruguay that is expected to progress to the semi finals.
Uruguay face underdogs Tahiti in their final group match, while Nigeria faces World and European champion Spain.
Nigeria coach Stephen Keshi said: "I think my players played well and played to instructions. It was just one minute's lack of concentration that made the difference. Otherwise it was good."
Spain, who thrashed Tahiti 10-0 earlier Thursday, leads Group B with six points, while Tahiti are bottom with none.
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