Substitute midfielder Mario Bolatti stabbed home the only goal five minutes from the end of a tense, foul-riddled match at the Centenario, ending Uruguay's hopes of a victory that would have put them through.
Maradona, whom fans and media had turned against after recent defeats, celebrated wildly on the touchline after the goal and wept and hugged members of his coaching staff in an outpouring of emotion at the final whistle.
"I want to dedicate this to all Argentines," he later told Argentine television. "I thank the squad."
Having replaced Alfio Basile as coach midway through the qualifiers, Maradona's credentials for the job had been widely questioned after his side lost to Bolivia, Ecuador, Paraguay and at home to Brazil.
Twice world champions Argentina finished the South American qualifiers in fourth place, the last of the automatic berths, consigning Uruguay to their third playoff in as many qualifying series.
Uruguay will face Costa Rica, the team that finished fourth in the CONCACAF region, over two legs next month for a spot in the June 11-July 11 finals.
Argentina joined Brazil, Chile and Paraguay as South America's representatives in the finals in South Africa. Uruguay needed a win to snatch the berth that Argentina took.
"We hade a unique opportunity (which) we didn't manage to take, but at least now we have the chance of the playoff," Uruguay striker Diego Forlan told reporters.
"Uruguay were tough rivals but we managed to impose our game and qualify, which gives us the calm to be able to work (until the World Cup)," Veron told Argentine TV.
Uruguay defender Martin Caceres was sent off in the 81st minute for bringing down Jonas Gutierrez, his second yellow card offence. His team mate Cristian Rodriguez was sent off right at the end, four minutes into stoppage time, for violent conduct.
ARGENTINE CONTROL
Argentina, who had struggled with the inexperience of Maradona as coach and his inconsistencies in selection, survived some early scares.
Forlan sent fellow striker Luis Suarez through the middle in the fourth minute and Argentina's keeper Sergio Romero came out of goal sharply to meet him, the striker getting a rebound that went wide.
Gradually Argentina, with Juan Sebastian Veron pulling the strings, doused the Uruguayans' fire and took some control with their possession game but never really put Uruguayan keeper Fernando Muslera in danger until the final quarter of an hour.
Forlan went close after the interval with a shot from the edge of the box as Uruguay, also twice world champions, made a similarly forceful start to the second half.
Argentina, playing better than in their previous seven qualifiers under Maradona, again took control with some precise passing in midfield looking for the telling breakthrough.
Muslera went down to save at striker Gonzalo Higuain's feet from Lionel Messi's pass and Uruguay captain Diego Lugano headed wide at the other end.
The breakthrough came when Bolatti, who had come on for Higuain five minutes earlier in his first qualifier and only his third international, found the net from close range following Veron's ball into a packed area from the left.
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