The Hondurans needed a victory and either a loss or draw by Costa Rica to advance and a goal by American Jonathan Bornstein in the fifth minute of stoppage time gave USA a 2-2 draw with Costa Rica.
Costa Rica appeared headed for South Africa until Bornstein's dramatic late intervention, with the draw sending the Ticos into a two-legged play-off with Uruguay.
Honduras shook off the disappointment of their first home loss of the campaign - a 3-2 heart-breaker to the USA suffered on Saturday to defeat their arch rivals in San Salvador. Pavon scored the only goal the Hondurans needed in front of a crowd of 30,000 at Estadio Cuscatlan stadium to edge through on goal difference.
USA's late equaliser confirmed the Americans position at the top of the CONCACAF standings with Trinidad and Tobago holding Mexico 2-2 in the other match.