Hector Moreno headed home a corner kick in the 64th minute and Hirving Lozano chipped a shot over the Chilean goalkeeper's head less than a minute later to put the contest out of Chile's reach.
The win is the first for the 56-year-old Argentine Martino, who led Atlanta United to the MLS Cup last season before being named as Mexico's head coach in January.
(Reporting by Rory Carroll; editing by Sudipto Ganguly)