Going into the last round of games of the opening phase of the season, the trio were battling it out with Tijuana and Chiapas for the right to join America, Santos Laguna, Cruz Azul, Leon and Toluca in the play-offs.
And they all picked up vital 1-0 victories, with Morelia beating Puebla at home on Saturday, while Queretaro and Tigres UANL won at Pachuca and Atlas respectively on Sunday.
Fellow hopefuls Tijuana were hammered 5-0 at Leon, while Chiapas lost 2-0 at Atlante.
Morelia finish the Apertura in sixth spot thanks to Enrique Perez's injury-time winner at the Estadio Generalisimo Jose Maria Morelos y Pavon.
There was also late drama in Queretaro's victory at Pachuca, as Wilberto Cosme's 90th-minute strike secured seventh for Ignacio Ambriz's side.
Tigres UANL, meanwhile, took full advantage of Chiapas' defeat to leapfrog them into eighth thanks to Facundo Erpen's second-half own goal at the Estadio Jalisco.
Elsewhere, Apertura leaders America made it three games without a win as they dropped points at home in the Liga MX for the first time this season in a 1-1 draw with Toluca on Saturday.
Former Sunderland and Real Zaragoza defender Paulo da Silva gave the visitors the lead in first-half injury time, before Narciso Mina spared America's blushes with an equaliser 68 minutes in.
Second-placed Santos Laguna were also held to a home draw, as they twice had to come from behind to finish 2-2 against Veracruz.
Cristian Martinez Borja put Veracruz ahead in the first half, before Javier Arozco equalised with 82 minutes gone. Oscar Mascorro promptly restored the away side's lead before Eduardo Herrera snatched a point for Santos in the last minute.
Elsewhere, bottom-placed Pumas UNAM fought back from two goals down to earn a creditable 2-2 draw at home to Cruz Azul, while Monterrey came from a goal behind to beat Guadalajara 2-1.
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