Colombian star Mendoza doubled the lead in the 48th minute, racing on to an Elano Blumer through ball, rounding Steve Simonsen and finishing it at ease.
Chennaiyin manager Marco Materazzi will have to re-group his squad after the loss to NorthEast United.
The lack of finishing upfront led Atletico to their second successive loss, the first time they have suffered this fate in the two-year history of the ISL.
NorthEast United look for a second upset against Atletico de Kolkata after beating Chennaiyin FC 2-0 in their last encounter. ATK go in as current favourites.
Leo Moura and Gregory Arnolin scored once in each half as FC Goa beat Kerala Blasters FC 2-1 to go top of the points table in their Indian Super League.
Before the half time, NorthEast head coach Cesar Farias and his Chennaiyin counterpart Marco Materazzi exchanged heated words from their respective touchlines.
Mumbai’s big hopes of turning a new leaf at their home venue after the first two away games came to naught when they were thrashed 2-0 by Chennayin FC.
The team from the eastern part of the country has lost all its three outings so far, losing 1-3 to Kerala Blasters and FC Goa and 0-1 to FC Pune City.
The defending champions were off to a dream start at their own backyard. Five minutes into the game they made their intentions quite clear
This was Dynamos’ second win in three outings, while the Pune suffered their first defeat at home at the Balewadi Stadium.
Pune will look to use their home conditions to best effect and hold on to their winning momentum against NorthEast United
Dynamos lost their first match of the tournament away against FC Goa 0-2 while Chennaiyin were beaten 2-3 at home by title holders Atletico de Kolkata.