Honduran players stood on the field awaiting news of the group's other vital game and broke down in emotional celebration after learning a late equaliser had earned the United States a 2-2 draw with Costa Rica.
That result pushed Costa Rica into a play-off with Uruguay, beaten 1-0 by Brazil in South American qualifying, while Honduras gained CONCACAF's final automatic berth.
"We knew is would be a very tight game with an El Salvador team that is very well drilled, but that's football," said Honduras coach Reinaldo Rueda.
"Today it's the Honduras fans' and their team's turn to celebrate, thanks to the work of many years.
"Now we have months of work, months of matches and let's hope this victory works out for the good of all," he added.
Honduras's one and only previous World Cup finals appearance was in 1982 and fittingly it was their 36-year-old striker Carlos Pavon who scored the decisive goal on Wednesday.
Pavon, who played in qualifiers for the 1998 World Cup and missed a late penalty in Saturday's 3-2 loss to the United States, was seconds away from ending his career without appearing in a World Cup finals but has earned his chance after a night of drama.
Honduras, looking nervous and edgy, had few chances before they grabbed the lead through Pavon's header in the 64th minute from a beautiful David Suazo cross.
The victory - the first home loss for El Salvador in qualifying - would not have been enough had Costa Rica hung on to their lead against the United States.
But the tense moments of waiting for news from Washington ended in joy for the Hondurans when the scoreline came through.
Honduras suffered political upheaval following a military coup in June but Rueda said his team's achievement was a success for the whole country and the "happiness of the people."
