Defending champions America made it two victories from two matches, while Seattle Sounders and DC United also won.
America's title defence remains blemish-free after the reigning CONCACAF Champions League winners edged Walter Ferretti 1-0 on Wednesday.
Ecuador international attacker Michael Arroyo was the difference at the Estadio Azteca, with his 71st-minute strike enough to see America to their second win from as many matches in the continental tournament.
Arroyo capped a well-executed set-play by firing the ball low past Walter Ferretti goalkeeper Denis Espinoza from outside the penalty area 19 minutes from the end in Coyoacan, Mexico.
America, who beat Montreal Impact in the 2014-15 Champions League final, top Group E with six points.
Seattle Sounders produced a memorable fightback to overcome Paraguayan visitors Olimpia 2-1.
The Sounders, who played out a 1-1 draw against MLS rivals Vancouver Whitecaps last time out in Group F, appeared destined for defeat following Alberto Elis' fifth-minute opener.
But substitute Brad Evans had other ideas, netting a 97th-minute penalty after fellow second-half introduction Erik Friberg has equalised seven minutes earlier in Seattle.
Meanwhile, in-form DC United left it late as they kicked off their campaign with a 1-0 victory at Arabe Unido in Panama.
The Group H fixture was petering out for a draw until Miguel Aguilar broke the deadlock in the 85th minute.
Aguilar controlled the ball just outside the area before poking beyond Miguel Lloyd with five minutes remaining as United - top of the Eastern Conference in the MLS - made a winning start.