Fans who kept a safe distance from the chaos filmed the extraordinary moment the referee strolled around the center circle with the weapon in his hand.
The tense scene occurred during an amateur match in the Honduran town of La Jigua in western Honduras.
According to local reports, the unnamed referee brandished the pistol to protect himself from enraged supporters who believed he should have awarded their team a penalty.
At the end of the game, as he was being jeered by the enraged fans, a relative is said to have handed him the weapon.
Shots could be heard throughout the home-made video, but it was unclear where they came from.
One fan was overheard insulting the referee by calling him a son of a b****, despite the fact that he appeared to make the right decision by remaining in the stands.
There were no injuries reported as a result of the standoff.
Fans captured the extraordinary moment the match official strolled around the center circle with the weapon in his hand.
The match official has not been identified, and it is unclear whether he will face disciplinary action as a result of his radical decision.