A pro-American crowd of 24,650 chanted "Dos a cero!" at the start.
Mexican supporters yelled "Dos a uno!" as they left.
Rafa Marquez scored a tiebreaking goal on a header in the 89th minute, giving Mexico a 2-1 victory Friday night and its first victory at the United States in World Cup qualifying since 1972.
After winning four straight home qualifiers against Mexico by 2-0 scores — all in Columbus — the U.S. hoped to open the final round of the North and Central American and Caribbean region with another victory. Instead, the Americans began the hexagonal with a loss for the second straight cycle, and they play Tuesday night at Costa Rica, where they have never won in qualifying.
"It gets a sense of anger in us. It gets a sense of absolutely urgency," U.S. coach Jurgen Klinsmann said. "It's not a problem, but it's obviously disappointing."
Miguel Layun put Mexico ahead in the 20th minute, but Bobby Wood tied it in the 49th.
The U.S. dominated the second half before the 37-year-old Marquez, unmarked and drifting across the penalty area at the near post, got a glancing nod on Layun's corner kick. The Mexican captain lifted the ball over goalkeeper Brad Guzan for his 17th international goal.
Mexico's previous win at the U.S. in qualifying was also by a 2-1 score, at the Los Angeles Coliseum.
"I think we deserved this match," Layun said. "We were focused."
Klinsmann said John Brooks was supposed to mark Marquez on the corner kick. Jozy Altidore blocked the defender from getting there.
"We lost him there. Individual mistake," Klinsmann said.
The Americans had been 30-0-2 at home in qualifying since a 3-2 loss to Honduras at Washington's RFK Stadium in September 2001.
"They're very good in terms of when they have a little time circulating the ball, and they start to find space," American captain Michael Bradley said.
Guzan had lost the U.S. goalkeeper job to Tim Howard, who started at the last two World Cups. But Howard pulled a muscle in his right leg on a goal kick and was replaced in the 40th minute.
Howard was to have a scan Saturday, a day before the U.S. travels, and Klinsmann said Howard likely will miss the match at Costa Rica.
"He knows it's not looking that good," Klinsmann said.
The top three teams in the six-nation round qualify for the World Cup, and the fourth-place country advances to a playoff.
With the U.S. struggling early in what Klinsmann called a 3-4-3 formation, Mexico could have led 3-0. Howard tipped Jesus Corona's 10th-minute shot off a post and Carlos Vela's 25th-minute header hit a crossbar.
"Out midfielders didn't get into the one-on-one battles we expected them to," Klinsmann said, citing Jermaine Jones and Bradley.
After switching to a more familiar 4-4-2 in the 27th minute, the Americans began to find their rhythm, and Wood scored off a pass from Altidore.
It was 44 degrees at game time, half the 90-degree temperature for the 2013 match in Columbus, when the U.S. clinched its seventh straight World Cup berth.
Mexico went ahead after Bradley and Giovani dos Santos battled for the ball 30 yards out. The ball skipped to Layun, who took a touch, and his right-footed shot deflected off Timmy Chandler past Howard's left for his fourth international goal in 46 appearances,
Wood tied the score after Brooks forced a turnover. Altidore turned his defender and passed to Wood, who took two touches as he split defenders. His 8-yard, left-footed shot deflected off a leg of Layun for his eighth goal in 28 international appearances. Wood also scored against Mexico last fall during an extra-time loss in the playoff for a berth in the 2017 Confederations Cup.
Altidore and Wood have combined for seven goals in 11 games they've started together.
Notes: All three visiting teams had victories in their openers. Costa Rica won 2-0 at Trinidad and Tobago on goals by Christian Bolanos in the 65th and Ronald Matarrita in second-half injury time, and Panama won 1-0 at Honduras on Fidel Escobar's 22nd-minute goal. ... CONCACAF and Fox extended their Gold Cup agreement to cover the 2017 and 2019 tournaments. ... Mexico's Carlos Salcedo is suspended for Tuesday after receiving two yellow cards late in the match.