Forlan sent his shot high into the roof the net in the third minute of injury time after Ecuador goalkeeper Marcelo Elizaga upended Edinson Cavani.
The win hoisted Uruguay above Ecuador into fifth place in the 10-team South American qualifying group with 24 points from 17 games and a final match at home to Argentina on Wednesday.
Ecuador, who have 23 points, dropped from fourth to sixth and visit already-qualified Chile in their last game.
The top four teams qualify directly for South Africa next year and the fifth plays off against a team from CONCACAF for another place.
Ecuador appeared to have broken Uruguay's resistance when Manchester United midfielder Luis Antonio Valencia headed them in front after 68 minutes, meeting Jefferson Montero's cross at the far post.
The Uruguayans had apparently been struggling with the high altitude at 2,800 metres above sea level and had been taking their time over free kicks and throw-ins since midway through the first half.
Instead, they hit back immediately when Forlan broke down the left and found Luis Suarez, who placed a low shot into the bottom corner from close range.
Ecuador, attempting to qualify for their third successive World Cup, lost their composure and threw themselves forward and left spaces at the back for Uruguay to exploit.
