The Estadio Nacional Julio Martinez Pradanos hosts could not break down the visiting San Marcos in the opening 45 minutes, but coach Martin Lasarte deployed the game-changing substitution at the break.
With Gonzalo Espinoza sidelined with a broken collarbone, Universidad needed some midfield grunt - and Gustavo Lorenzetti's inclusion for the second half gave the home side an edge.
Nine minutes later, Universidad hit the front when Rubio converted from a cross in from the left, before San Marcos' fate was virtually sealed when goalkeeper Pedro Carrizo was sent off in the 74th minute.
Rubio's second goal, in injury time, made sure of the points for Lasarte's men, ahead of their El Clasico with Colo Colo on October 19.
It will be a top-of-the-table derby, as Colo Colo were 1-0 winners over Universidad de Concepcion, who fell to a third straight defeat.
O'Higgins (15 points) were the highest-ranked side to stumble at the weekend, and it cost them three spots in the table as they fell to eighth after a 1-0 loss at home to Palestino.
Their conquerors were one of the three sides to jump them in the table, along with Huachipato (fourth, 17 points) and Union La Calera (seventh, 15).
Huachipato were 3-0 victors at Universidad Catolica, and Union La Calera had a 2-1 home triumph over Cobresal.
Audax Italiano made it two wins in their past three, downing Deportes Iquique 2-1 to climb to 10th.
Iquique remain equal on seven points with Cobresal and bottom-placed Cobreloa, the latter beaten 2-1 at home to Barnechea - who climbed to 14th.
Cobreloa were left bottom of the table after Antofagasta (eight points) beat Nublense 2-0 for just their second win of the Apertura phase.
