"We're all happy because the truth is it's been a hard road," striker Edinson Cavani said after Uruguay's 18th match of the qualifying campaign. "We have to enjoy it."
Left-back Martin Caceres suggested that winning the first leg by such a big margin had made it harder to concentrate in the second.
"After winning 5-0 it was going to get complicated, we knew we had to take the match seriously," he added. "We'd have liked to give the crowd a triumph and at least one goal to shout about but it wasn't to be, that's football."
Despite needing to score at least five to have any hope of overturning the deficit, Jordan defended deep and in numbers on Wednesday, denying the South Americans scoring chances and making sure there would be no repeat of the 5-0 mauling.
The closest the home side came to scoring was when centre-back Diego Godin headed against the bar just before half-time, but the lack of goals failed to dampen celebrations on the pitch or among the crowd of 60,000 in the stands.
"(Jordan) got what they wanted, a dignified role and a result that I suppose for them is very important," coach Oscar Tabarez said.
"We must accept ... that the main reason why we couldn't win was our rivals' good tactics."
Jordan's Egyptian coach Hossam Hassan was pleased with his team's reaction to their punishing defeat at home.
"We played very well, we met a very good team, very strong, with players from different parts of the world," Hassan said.
"I want Uruguay to have a good World Cup in Brazil."
Before kick-off, the crowd at the Centenario were treated to a video of Alcides Ghiggia's winning goal when Uruguay upset Brazil 2-1 at the Maracana to win their second World Cup in 1950, the last time their northern neighbours hosted the finals.
The 86-year-old, the sole survivor of that "Maracanazo" team, also spoke to the crowd ahead of the game.
"At the Maracana (final) there were 30 Uruguayans," he said in the centre circle. "Today I have the luck to celebrate with all these people here and it's very emotional for me."
Jordan's packed defence gave 2010 semi-finalists Uruguay few openings.
Cavani, who scored a sublime free kick in the first leg, had two efforts that went over the bar while Luis Suarez worked tirelessly to find openings but often found himself forced out wide.
Uruguay captain Diego Lugano headed a corner wide of the far post just past the hour and Jordan took heart from the scoreless first half and were more daring after the break.
It was the fourth World Cup qualifying campaign in a row in which Uruguay went into a play-off, having finished fifth in the South American group behind Argentina, Colombia, Chile and Ecuador.
Uruguay reached the 2002 finals by beating Australia, but lost to the same opponents in the campaign for Germany 2006.
They went to the 2010 finals in South Africa after overcoming Costa Rica.
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- Edinson Cavani