Goals from Uriel Antuna and Raul Jimenez were enough for Tata Martino's side, with Mexico now securing their eighth consecutive qualification.
With the United States and Costa Rica facing off for the third automatic spot in CONCACAF qualifying, El Tri only realistically needed a draw to book an automatic berth in Qatar.
It was a dominant opening however, and Mexico were able to capitalise early to dispel any growing anxiety. Antuna opened the scoring in the 17th minute, dispatching the rebound after Nestor Araujo's powerful header from an Alexis Vega corner.
Running onto a ball behind the defence, Antuna then won his team a penalty in the 42nd minute. To essentially put the game beyond El Salvador's reach and secure his team's place in Qatar, Raul Jimenez calmly converted from the spot, sending Mario Gonzalez the wrong way.
With the win, El Tri finished the third round of qualification on 28 points, equal on points with first-placed Canada but with a lower goal difference.