Rivals Atletico San Luis scored the lone goal of the second leg in extra time to clinch the title and a spot in the first division - the second time they have left Maradona empty-handed in two consecutive finals.
"I nearly died... But it's fine. I'm sad for my boys, though," Maradona said after the match.
The Argentine great and his team faced a tough task heading into the second-leg match, having been held 1-1 in the first leg at home in Culiacan, in the northwestern state of Sinaloa.
They managed to hold Atletico to 90 goalless minutes playing away in the central city of San Luis Potosi.
But Spanish defender Unai Bilbao slotted in the winning goal for the home team in the 103rd minute, after Dorados 'keeper Gaspar Servio failed to clear a free kick.
The loss ended a 14-game unbeaten streak for Dorados, who faced a hostile crowd of nearly 25,000 that booed Maradona relentlessly.
Maradona, 58, took the coaching job at the Sinaloa-based club in September -- amusing skeptics who questioned why the 1986 World Cup champion, who has publicly battled various addictions, would move to a place better known for drug cartels than football.
But he has answered his critics by coaching the struggling Dorados to back-to-back finals, both against San Luis.
San Luis defeated Dorados 4-3 on aggregate in the fall season finals in December.
Having now won the spring finals, too, the club -- an affiliate of Atletico Madrid -- gain automatic promotion to the first division. Had they lost, they would have faced a playoff against Dorados to decide which won promotion.
Maradona can legitimately boast to having turned Dorados around: they were in 13th place in their 15-team division when he arrived.
But the dream of winning a title as coach still eludes him, after stints managing the Argentine national team and various clubs in Argentina, the Middle East and now Mexico.
In April, he said he planned to leave Dorados at the end of the season, alleging the league's referees were biased against him.