As reported by ESPN Mexico, 20-time Grand Slam champion Federer defeated world No. 7 Zverev 3-6, 6-4, 6-2 in front of the record-setting crowd, which was significantly higher than the previous record of 35,681, set when Serena Williams took on Kim Clijsters in Belgium in 2010.
Saturday's match marked the first time Federer, 38, had played in Mexico since he was a junior, and was part of the Swiss' South American tour, which also included meetings with Zverev in Chile and Argentina.
A scheduled match in Colombia was called off due to social unrest in Bogota, where the contest would have taken place.
Federer will have a chance to break the new record as early as February, when he faces Rafael Nadal in an exhibition match in South Africa.
The clash will take place at the Cape Town Stadium, which has a capacity of 55,000, and will be preceded by a doubles contest in which Federer will partner Microsoft founder Bill Gates, while Nadal pairs with South African comedian Trevor Noah.