Mexico took a 12th-minute lead through striker Javier Hernandez and looked set to hand Spain defeat in their first outing since winning the World Cup in South Africa a month ago.
Spain coach Vicente del Bosque praised his side's attitude in the friendly, with players having little practice since their 1-0 World Cup final win over Netherlands in Johannesburg on July 11.
"We, who turned up with few training sessions, have behaved extraordinarily. It's just another match but it has big symbolic significance because we came here almost without preparation," Del Bosque said.
"Some of the (team) members only had yesterday's practice," he told the post-match news conference.
"We must give the players 10 (out of 10), they made no excuses for playing the minutes they were asked to."
Hernandez put Mexico ahead when he chased a ball into space, faced goalkeeper Iker Casillas, and with the Spain captain expecting a shot across his body Hernandez slotted the ball inside the near post.
"Mexico have a team of quality with young players who were a threat in attack throughout the 90 minutes," Del Bosque said.
SILVA BULLET
The Mexicans showed greater urgency than Spain and were worth their lead but the arrival of Xavi just past the hour injected some bite into the Spanish attack.
Playing their trademark short passing game at near walking pace in the first half, Spain had come closest when a venomous shot from Santi Cazorla rattled Guillermo Ochoa's crossbar.
Casillas had to make a diving save from midfielder Rafael Marquez before ceding his place to Victor Valdes in the second half.
Substitute Pedro, who came on in the 72nd minute, brought a good save from Mexico's substitute keeper Jesus Corona when he looked set to equalise three minutes from time.
Silva, however, made no mistake two minutes into added time when he ran on to a fine through ball from Xavi to shoot past the diving Corona.
Spain became the latest world champions not to win their first match after lifting the FIFA trophy. Brazil in 1994 were the last team to win a match immediately after their World Cup success.
Before kick-off, Casillas paraded the World Cup to applause from the 100,000 crowd in the Azteca.
He was handed a trophy at the end of the match in recognition of the Spanish team's visit, which is part of Mexico's Bicentennial celebrations.
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