Xavier Baez and Jonny Magallon scored in each half of the semi-final second leg to give the Chivas a 3-1 aggregate win as they made the most of a goodwill gesture to invite them into South America's top club tournament.
They became only the second Mexican team to reach the final since the country's clubs were first invited to take part in 1998.
Last year, Guadalajara and fellow Mexicans San Luis withdrew from the tournament when their opponents declined to travel to Mexico for second round matches because of the H1N1 flu outbreak.
The Mexican Football Federation angrily announced their teams would not take part in future but the row was quickly patched up and the two teams were given automatic places in the last 16 of this year's tournament as compensation.
As a result, Guadalajara, beaten semi-finalists in 2005 and 2006, needed only six matches the reach the final.
Universidad de Chile started the match as favourites after their 1-1 away draw last week but left too many gaps at the back as they threw players forward.
The warning signs were evident when Guadalajara striker Omar Bravo had two chances to score in the first five minutes.
The Chivas, who field only Mexican players, went ahead in the 22nd minute when Baez scored with a long-range shot.
Jose Contreras and Rafael Olarra hit the bar for the Chileans in a three-minute spell before the break but it was Guadalajara who struck again when defender Magallon headed their second goal seven minutes after half-time.
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