Lopez headed the ball into his own net trying to clear a cross from midfielder Damian Alvarez a minute before half-time in the semi-final second leg at the Universitario stadium in the northern city of Monterrey.
"Fortunately we got the result with their own goal and now we're going to the final," Tigres defender Hugo Ayala told television broadcasters Televisa.
It was the only goal of the tie after Queretaro, playing in the eight-team knockout phase of the championship for the first time, held Tigres 0-0 at home in midweek.
Tigres were also awarded a penalty on the hour but forward Hector Mancilla's kick was saved by goalkeeper Liborio Sanchez, who was again his team's best player.
Queretaro had Michel Vazquez sent off three minutes into added time for a foul on midfielder Manuel Viniegra.
Tigres will be looking for their second league title and first since the 1981/82 season.
Santos have three titles, all since the introduction in 1996/97 of two championships per season, with their last the 2008 Clausura.
They reached the final by beating Morelia 3-2 in a thrilling semi-final second leg on Saturday.
The aggregate score was 4-4 with Santos qualifying by virtue of having finished higher in the league standings before the knockout phase.
