Diego de la Torre and Raul Nava each scored twice for Toluca in the Group B top-of-the-standings clash. Marathon is second with six points, three more than D.C. United.
D.C. United will host Marathon in a crucial match Thursday night.
Costa Rican veteran Rolando Fonseca scored a goal in each half for Comunicaciones.
Mexican teams lead all but Group A, where Panama's Arabe Unido hosts a one-point lead over Pachuca.
The only MLS team currently in a position to advance to next year's knockout stage is the Columbus Crew, which trails Cruz Azul by one point in Group C.
The group stage concludes with matches Sept. 22-24, Sept. 29-Oct. 1 and Oct. 20-22.
GROUP A
TEAM GP W T L GF GA P
Arabe Unido 3 2 1 0 6 2 7
Pachuca 3 2 0 1 8 4 6
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Houston Dynamo 3 1 1 1 4 4
Metapan 3 0 0 3 0 7 0
GROUP B
TEAM GP W T L GF GA P
Toluca 3 3 0 0 11 1 9
Marathon 3 2 0 1 6 9 6
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D.C. United 3 1 0 2 3 6 3
Jabloteh 3 0 0 3 1 5 0
GROUP C
TEAM GP W T L GF GA P
Cruz Azul 3 2 1 0 10 3 7
Columbus Crew 3 2 0 1 3 5 6
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Saprissa 3 1 0 2 3 4 3
Puerto Rico Islanders 3 0 1 2 4 8 1
GROUP D
TEAM GP W T L GF GA P
UNAM 3 2 1 0 8 3 7
Comunicaciones 3 2 0 1 4 2 6
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Real Espana 3 1 0 2 2 7 3
W Connection 3 0 1 2 3 5 1



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