A goal in each half - through Xavier Baez and Jonny Magallon - saw Guadalajara claim a 2-0 second-leg win and a place in the final. Jose Luis Real's side will meet either Internacional or Sao Paulo, with the former leading 1-0 ahead of the second leg.
A mistake by Universidad's Miguel Pinto helped Baez open the scoring in the 22nd minute, as the goalkeeper fumbled the midfielder's shot from outside the box. The Chilean team had two opportunities to equalise but Juan Manuel Olivera hit the crossbar with a right-foot shot and Rafael Olarra headed against the woodwork.
Pinto made a superb save from Magallon in the second half after Baez's cross, but was powerless as Magallon fired in the visitors' second from the rebound. Miguel Angel Ponce cleared off the line after Mauricio Victorino's header as Universidad went close to an equaliser. They needed three goals to book their place in the final, but could not manage one as Guadalajara held on to progress.
Guadalajara entered the tournament in the round of 16 after being disqualified from the competition last year due to the swine flu epidemic.
They will become the second Mexican side to play in the finals and midfielder Edgar Mejia is excited at the prospect. "We are very happy," he told Fox Sports. "We were looking forward to this.
"We played a very intelligent match. There is one step left. We are calm and aware of the importance the next step has. We must do our best."