Needing to overturn a five-goal deficit in goal difference to finish top heading into the play-offs, they started like they meant to do just that with two goals in the first two minutes from Alfredo Moreno and Duvier Riascos.
But they could not find another in the remaining 88 minutes, so had to be content with second, sandwiched between Toluca and Leon.
Unam Pumas beat Atlante 3-2 but it was not enough to book them a play-off spot.
Either side could have snuck into the play-offs with a really big win and it was Atlante who started brightest, Esteban Paredes putting them ahead in the fifth minute, but goals from Luis Fuentes (30) and Marco Palacios (39) turned the game before half-time.
Palacios then put the ball in his own net after 51 minutes, before Martin Bravo sealed a win for the Pumas which ultimately proved academic.
Luis Landin (12) scored the only goal as Queretaro, who had Gonzalo Pineda sent off in the 68th minutes, won 1-0 at Puebla.
The play-offs begin next weekend with the first of two legs of the quarter-final matches.