Javier Aguirre's side led 1-0 at the break thanks to an own goal from El Salvador defender Marvin Gonzalez and although they dominated possession it was not until Cuauhtemoc Blanco's 71st minute goal that the Mexicans began to feel comfortable.
The result assures Mexico will appear at their fifth straight finals and completes an outstanding turnaround after their poor start to the campaign with three defeats from their opening four games.
"I am so happy, it is time to celebrate," said skipper Rafael Marquez. "This is a great team and Javier Aguirre is a great coach. We have got the job done."
Mexico move to 18 points while El Salvador (eight) are eliminated. The United States (16) face Honduras (13) later on Saturday with both teams in contention.
Costa Rica (12) are also still fighting for qualification when they host already eliminated Trinidad and Tobago.
Aguirre had talked of "war" in the build-up but the game began in comical fashion with play delayed after just three minutes due to a swarm of bees around the El Salvador goal.
The 100,000 crowd at the Azteca stadium looked on bemused as officials sprayed the bees with fire extinguishers during a delay of over seven minutes before play resumed.
Mexico went ahead when Blanco and Guillermo Franco combined on the edge of the area and in the resultant scramble Gonzalez poked the ball into his own goal.
Blanco had been an injury doubt for the Mexicans and the 36-year-old showed his significance to the team with a typically influential display.
The forward made it 2-0 when he finished off a beautiful flowing move, involving Franco and Carlos Vela and celebrated by racing over to Aguirre and hugging the coach on the sideline.
Substitute Francisco Palencia made it 3-0 with a fierce strike in the 84th minute to start the celebrations in earnest although a rocketing free-kick from Julio Martinez pulled one back for El Salvador.
Mexico restored their three-goal advantage a minute from the end when Vela scored after some woeful defending from the unfortunate Gonzalez who back-headed straight into the path of the Arsenal forward.
The Mexicans will finish their CONCACAF campaign away to Trinidad and Tobago on Wednesday.
