The Uruguayans went through 2-1 on aggregate after winning the first leg in San Jose on Saturday, returning to the finals in South Africa next year after missing the 2006 tournament in Germany.
Substitute striker Sebastian Abreu headed home with 20 minutes to go to put Uruguay ahead, sparking huge celebrations by the home team, their bench and the packed Centenario terraces.
But just three minutes later midfielder Walter Centeno, the Costa Rica captain, restored the Central Americans' hopes of an upset when he stunned Uruguay with an equaliser.
The match was held up for nearly five minutes near the end because of fighting between a Uruguay camera crew near the touchline and the Costa Rica bench amid a nervous denouement dominated by Costa Rica but with near misses at both ends.
At the final whistle, the celebrations broke out again as the Uruguayans, who won the second of their world titles in 1950, released their emotions at the relief of having qualified.
"The qualification series was very tough and this match confirmed that," Uruguay coach Oscar Washington Tabarez told a television reporter.
Abreu said: "When Tabarez called me to go on, I was very happy and dreamed of this goal and I was able to help the team reach the World Cup."
Uruguay captain Diego Lugano told reporters: "It's incredible to have to suffer so much to get to a World Cup but it appears we're destined to that."
Uruguay reached the playoff by finishing fifth in the South American qualifiers and Costa Rica fourth in CONCACAF.
MISSED CHANCES
Uruguay failed to impose their authority on the game despite the lion's share of possession. They squandered a string of free kicks by playmaker Nicolas Lodeiro into the box and other chances from untidy attacks after two near misses early on.
In the fifth minute, Costa Rica keeper Keilor Navas dived to his left to turn away a shot by Diego Forlan from outside the box and a minute later a header from midfielder Sebastian Eguren went straight to him.
Just past the half hour Lodeiro played Luis Suarez in on the right but the striker shot first time over the bar.
Costa Rica midfielder Christian Bolanos gave Uruguay a scare nine minutes before the interval with a shot from the edge of the box that Fernando Muslera stretched to turn over for a corner.
Six minutes into the second half, a Lodeiro cross from the left found Eguren who rose above the defence but directed his header just wide.
Just before the hour, Forlan placed a good shot on target low to the right of Navas but the keeper dived and managed to turn it away at the foot of the post.
The tall Abreu's introduction in the 65th minute finally unlocked the Costa Rica defence when he rose to head defender Andres Scotti's high cross over Navas into the net.
Uruguay's nerves were rattled again, though, when Centeno shot home from close to the penalty spot after a poor clearance by the defence.
