The victory, coupled with Honduras’ 2-2 draw against Panama on Tuesday night, sends the Americans to next summer’s tournament in Brazil.
After withstanding Mexican pressure for the first 20 minutes, the U.S. settled into the match and got the breakthrough in the 49th minute when Johnson outjumped defender Diego Reyes to meet Donovan’s corner kick 8 yards out and head the ball past frozen goalkeeper Jesus Corona.
With Mexican shifting to an offense-minded 3-4-3 formation, the U.S. scored in the 78th following a throw in when Mix Diskerud threaded the ball across the goalmouth. Clint Dempsey touched it as it went by to Donovan, who poked it in from 2 yards.
The U.S. (5-2-1) moved into first place in the North and Central American and Caribbean finals with 16 points, one ahead of Costa Rica (4-1-3), which was held to a 1-1 tie at last-place Jamaica.
The top three teams qualify automatically. Mexico (1-2-5) is fourth and likely headed to a playoff against Oceania champion New Zealand.
U.S. players, many carrying large American flags on sticks, celebrated the victory with a lap around the field, saluting the fans the whole way. Then they went to the locker room to wait out the Honduras game.
Johnson nearly scored off Donovan’s cross in the third minute of the second half, but the pass was just ahead of him.
A minute later, the U.S. took just its second corner kick of the match. Jermaine Jones and Johnson both broke in from behind the penalty spot, and Mexico was slow to react as Johnson scored in 12th goal in 21 qualifying appearances.
Donovan’s goal increased his national team record to 57.
Dempsey missed a penalty kick in second-half injury time, just before the final whistle.
Dealing with an injury to midfielder Michael Bradley and yellow-card suspensions of defender Matt Besler, midfielder Geoff Cameron and forward Jozy Altidore, U.S. coach Jurgen Klinsmann had to make several changes from Friday’s 2-1 loss at Costa Rica.
Fabian Johnson shifted from midfield to the back line, and Clarence Goodson was among four new starters, joined by midfielders Kyle Beckerman and Alejandro Bedoya, and forward Eddie Johnson. Fabian Johnson strained his left hamstring and was replaced by Michael Parkhurst for the start of the second half.
Mexico dominated the first 20 minutes of the opening half and the last five, forcing goalkeeper Tim Howard to make several sprawling saves.
The first came seven minutes in, when American left back DaMarcus Beasley scuffed a clearance and nearly put the ball in his own goal.
Howard made a diving parry on Christian Gimenez in the 19th, and then two minutes later pushed Gimenez’s free kick over the crossbar. Howard was forced into another diving save on Giovani Dos Santos in the 44th, and then dived to knock a header over the line in injury time after Bedoya pulled down Dos Santos with a sliding tackle, earning a yellow card.
The first good U.S. chance was when Donovan’s free kick was knocked down Omar Gonzalez in the 14th, and Jermaine Jones volleyed over the crossbar.
Eddie Johnson’s header off Donovan’s corner kick was saved by goalkeeper Jesus Corona in the 32nd.