Mexico entered Friday's match at the Estadio Azteca desperate for their first victory at home in the fourth and final round of CONCACAF's World Cup qualifying system, after one win and five draws from their first six matches.
It started well for the hosts with an early goal to Oribe Peralta but second-half strikes in quick succession from Jerry Bengtson and Carlos Costly saw Honduras claim a stunning comeback victory; their first-ever win in Mexico.
The win took Honduras above Mexico into the third automatic qualifying slot for next year's World Cup finals in CONCACAF's fourth round.
Honduras have 10 points, while Mexico have eight and could drop to fifth if Panama defeat Jamaica later on Friday.
Mexico started brilliantly with Peralta and Giovani dos Santos combining to open the scoring in the sixth minute.
Peralta's flick allowed Dos Santos to burst away from the centre circle with the ball at his feet and the former Barcelona and Tottenham midfielder sprinted into the box, before squaring a pass back to Mexico's lead striker, who side-footed home into an empty net.
The hosts dominated the first half in Mexico City with 69 per cent possession but the lead remained at just 1-0 at the break with the home side only managing two shots on target, while Honduras failed to test Mexico's goalkeeper at all.
The introduction of Bengtson at half-time changed the match for Honduras, however, as the visitors started to attack with more purpose.
In the 64th minute, Mexican defender Carlos Salcido failed to head a cross clear of his penalty area and Costly brought the ball down, turned and unleashed a shot from the edge of the box.
Mexico's goalkeeper Jose de Jesus Corona could only parry the shot and Bengtson was there to convert the rebound.
Honduras sprang into the lead just two minutes later when Costly held off Diego Reyes to collect a long ball out of defence and the 31-year-old striker struck his shot across Corona and into the bottom corner of the net.
While Mexico had a couple of half chances in the final 20 minutes, they failed to truly test the visiting defence and Honduras held on for an historic victory.
