Santos extended its unbeaten streak to seven games overall and prevailed 7-3 on aggregate. It will play Monterrey, which beat Pumas UNAM 4-1 on aggregate after a 1-1 draw Wednesday night, in the final April 17 and April 24.
Toronto twice took lead on goals by Joao Plata, but Santos equalized on Gomez's fifth and sixth of the tournament before halftime.
Gomez, a member of the 2010 U.S. World Cup team, has scored in his last eight games for Santos. He has 11 goals this season.
Julian De Guzman tripped Christian Suarez in the penalty area, and Rodriguez converted the ensuing penalty in the 56th minute. His second penalty came in the 64th minute.