Their Portuguese coach Pedro Caixinha, whose side crushed Queretaro 5-0 in Thursday's first leg, suggested the success might help him with his ambition of working at a European club.
"This is the start of a cycle, I'm very happy at Santos and I think this process has a good future, but I have the ambition to reach the highest level of football, that is in Europe," Caixinha told reporters.
Queretaro scored all three goals in the first half, through midfielder Mario Osuna with a penalty, defender Yasser Corona with a header at a corner and striker Angel Sepulveda.
But even the introduction of Brazilian Ronaldinho for the last half hour failed to produce the two more they needed to take the Clausura championship decider to penalties.
Queretaro's veteran coach Victor Manuel Vucetich, who earned the nickname "King Midas" for his ability to win finals, was unable to touch gold this time and conceded his second loss to Santos in a title decider.
It was Vucetich's second defeat in seven Mexican league finals but he was full of praise for his players saying: "I feel motivated by the team's reaction, by their conviction, for keeping their pride and dignity."
Santos are the only team to have beaten Vucetich in a final, the first time in 2012 when he was in charge of Monterrey, the side he led to two of his five titles.
(Writing by Rex Gowar; Editing by John O'Brien)
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