Rueda, a former Colombia coach, was presented with his citizenship document by Honduran national congress president Juan Orlando Hernandez at a buzzing Estadio Olimpico, but the buzz went out of the occasion when Venezuela captain Francisco Flores scored a fine goal early in the second half.
Honduras failed to conjure an equaliser leaving their fans with little more than corners or free kicks near goal to cheer.
Rueda said fatigue in the final stages of the Honduran championship had affected some of his players' performances.
"We saw that many players who have been playing well in the league did not play well today," said Rueda, for whom the friendly was useful preparation for his team's opening Group H match against Chile in Nelspruit on June 16.
Despite the team's farewell, which included President Porfirio Lobo handing a Honduran flag to team captain Amado Guevara, the players were greeted by largely empty terraces at either end of the 41,000-capacity stadium.
"It's normal because it didn't coincide with pay day. It affected (us) quite a bit, the attendance could have been better," Rueda told the post-match news conference.
"Now we're going to become elitist and only follow (the team) when England, Germany, Brazil or France come here. Perhaps we didn't give our rivals due respect and they gave us a great lesson," he added.
The Hondurans, once the domestic championship is over in early May, will head for a pre-finals training camp in Germany that will include three warm-up matches against Azerbaijan, Belarus and Romania in Austria.
They also face favourites Spain and Switzerland in their group.
Rueda, who took charge of the team in 2007, was granted Honduran citizenship by the country's congress in an unanimous vote in the capital Tegucigalpa on Tuesday having steered the Central American country to their second World Cup.
