Club America opened the scoring in the second leg in the 18th minute when Oscar Rojas' cross banged off Arsenal defender Christian Diaz into his own goal.
Arsenal's Jose Calderon hit the post twice and Club America goalkeeper Guillermo Ochoa saved a strong header from Andres San Martin to keep the Mexican club ahead.
Juan Silva's volley gave Club America a 2-0 lead (4-3 on aggregate) after latching on to a lobbed German Villa pass. But then Andrizzi's strike finally brought a trophy to Arsenal.
Pachuca won the 2006 Copa Sudamericana with a final win over Colo Colo of Chile. In 2005, the Mexico's UNAM Pumas fell to Boca Juniors in a penalty shootout.