They qualified to Korea-Japan in 2002 by beating Australia, the same opponents who beat them ahead of the 2006 tournament.
They will join fellow South American teams Brazil, Chile, Paraguay and Argentina at the finals in South Africa.
"It was very tough," said Uruguay coach Oscar Tabarez. "This match mirrored the tie as a whole. I'm very happy. Fortunately, we made it, in spite of the way we did it.
"There is a lot to improve on. We'll do so and we'll have the World Cup to prove it. I'm very happy, mostly for the kids. The ones who are younger than eight-years-old have never seen this and now they can live it."
Captain Diego Lugano was disappointed Uruguay had to go through the play-offs, saying: "I am happy to qualify, but not for the way we've clinched it. It is unbelievable that we have to suffer this way."
Midfielder Alvaro Fernandez added: "We'll never make it into the World Cup comfortably, but it has a special taste."
Costa Rica coach Rene Simoes, who coached Jamaica in the 1998 World Cup, announced he will likely step aside from the position even if federation president Eduardo Li offers him a new deal.
"I spoke to the federation president before the match," he said. "He did not officially offer the job but left the doors open. However, four years is too much for me.
"I don't want four years anymore. I would like one and then to decide whether or not to go on. Coaching life is very difficult and I miss my family a lot."
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