The two teams met in a play-off that had more at stake than simply a place at the 1970 World Cup in Mexico and each side was subjected to abuse, xenophobia and hatred when playing in the other country.
After losing 3-0 in El Salvador, Honduras coach Mario Griffin wryly observed: "We're awfully lucky that we lost."
El Salvador progressed to the World Cup finals but neither side prospered from the Soccer War, as it has become known, which broke out less than three weeks after Honduras were eliminated.
The war lasted 100 hours and left an estimated 6,000 dead and 12,000 wounded.
The legendary Polish foreign correspondent Ryszard Kapuscinski covered the war and wrote afterwards: "In Latin America, the border between soccer and politics is vague.
"There is a long list of governments that have been overthrown after the defeat of the national team."
Last year Honduras's attempt to qualify for the World Cup finals took place amid a backdrop of political turmoil.
President Manuel Zelaya was forced into exile in July amid a power struggle over his plans for constitutional change. Roberto Micheletti was sworn in as interim leader, although Zelaya returned to Honduras in September and sought sanctuary in the Brazilian embassy as he tried to return to power.
It was a delicate situation that could easily have become far worse when Honduras, who are represented in the Premier League by Tottenham's Wilson Palacios and Wigan duo Hendry Thomas and Maynor Figueroa, travelled to El Salvador for their final qualifier on 14 October.
A Honduras victory combined with the United States avoiding defeat against Costa Rica would ensure their place at the finals in South Africa 2010.
Honduran football association president Rafael Callejas was inside the Estadio Cuscatlan in San Salvador and saw veteran striker Carlos Pavon put his side in front just after the hour but news of the score between the US and Costa Rica was scarce. The game was not broadcast inside the stadium and the reception on both of Callejas's mobile phones was terrible.
He eventually found out that Costa Rica had raced into an early 2-0 lead and later discovered that Michael Bradley had pulled a goal back for the US after 71 minutes.
"I was happy we were winning but sad because I knew that Costa Rica were still in front," Callejas told me. "There was a lot of speculation and it was not until a minute after the final whistle that all the Hondurans inside the ground found out the US had scored a late equaliser, meaning that we had qualified."
It was the first time since 1982 they had made it to a World Cup finals.
Perhaps more significantly, in a reversal of the events of 1969 it seems that 40 years on their footballing triumph played its role in preventing an outbreak of violence.
"If we had not qualified for the World Cup the differences in Honduras would have become enhanced and probably we would have had high levels of violence," added Callejas.
"People were tranquilised by the game, it gave them hope and happiness."
Callejas should have a better understanding than most of the relationship between politics and football in Honduras, having been president of the nation from 1990 to 1994.
He believes Honduras to be a country that lives and breathes football and noted: "Everybody is not only a fan but they are also a reporter, director and coach."
And the 66-year-old describes the team's qualification for South Africa as a balm that brought Honduras together at a time when it was badly fracturing.
"You cannot imagine how happy people were - they forgot everything," he said. "There were groups that wanted us to lose until we won and then they were also happy."
Photographs showed the ousted Zelaya celebrating inside the Brazilian embassy, while Callejas claimed the populace was so keen to celebrate with their heroes that the team feared for their safety on their return from El Salvador.
"We could not organise anything," stated Callejas. "We could not even get on a bus because every time we tried people just climbed on it and ran in front of it.
"There was no way the police or army could protect the players. In the end we parked in front of the presidential palace - not necessarily to see the president but to run away from all that was happening and protect the players."
Micheletti came out to greet the triumphant squad and Callejas, doubtless an old hand at such matters, fully admits that the maximum possible political gain was made of the situation.
An election held in Honduras in November was won by Pofirio Lobo, a member of the opposition to Zelaya's Liberal Party. The legitimacy of it was questioned by many observers but Lobo was sworn in as president in January and Zelaya left for exile in the Dominican Republic.
The political crisis in Honduras seems to be over and Callejas is now focused on the World Cup, when his team will try to qualify from a group that also comprises Spain, Chile and Switzerland.
At the end of his report on the Soccer War, Kapuscinski concluded: "The only chance small countries from the Third World have of evoking a lively international interest is when they shed blood. This is a sad truth but it is so."
But whatever happens in South Africa, the Honduras team has already shown the power that football has to unite people.
Exclusively by: Paul Fletcher | BBC Correspondent