Inter, also champions in 2006, won 5-3 on aggregate after a 2-1 first-leg victory on Guadalajara's synthetic pitch last week.
The match was marred by a disgraceful finish in which Guadalajara players went looking for a fight with rival players as the pitch filled with police, reserves of both teams and dozens of others.
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The Chivas of Guadalajara shocked Inter by taking the lead through midfielder Marco de La Mora just before the interval.
Inter replied with goals from striker Rafael Sobis and substitutes Leandro and Giuliano in the final half hour before Omar Bravo scored a second for the Chivas in stoppage time.
"It's a unique moment, every player wants a moment like this," captain Bolivar told reporters on the pitch before raising the cup. "It's historic to be able to lift that trophy."
Guadalajara took the lead when Bravo headed a cross back into the danger area where De La Mora swiveled in front of the static Indio to hit a chest-high ball into Renan's top right corner.
De la Mora had served warning midway through the first half that the Chivas would try for goal with every chance they got, however far out, shooting just wide from 30 metres.
SOBIS EQUALISER
Early in the second half Michel did well to thwart Sobis at his feet as he tried to round the keeper after running onto a superb through ball from left-back Kleber.
Sobis equalised in the 61st minute from another fine attack by Kleber, reaching the defender's low cross from the left to poke it past the goalkeeper into the net.
"Alecsandro has different positioning (from Sobis). We hardly practiced (that move) but it worked out in the match," Kleber told reporters of the equaliser.
Sobis, who scored twice in the 2006 final, is usually a reserve who played because Alecsandro was injured.
"Two Libertadores titles with the team of my heart is just too much," Sobis said. "A bit of that goal is for Alecsandro."
Leandro, just on for Sobis, skipped past two defenders on the halfway line with his first touch and raced away to score 13 minutes from time.
Giuliano, Inter's top scorer, took his tally to six when he made sure of victory with their third a minute from time. He scored two less than the competition's leading marksman, Thiago Ribeiro of Cruzeiro.
Inter will now go for a second Club World Cup title in Abu Dhabi in December. In 2006, Inter were crowned champions when they beat Barcelona, winners last year, in the final in Japan.
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