Two goals in two minutes from substitute Richard Ruiz and Colombian Duvier Riascos midway through the second half gave the small border town club a shock 2-0 win away to favourites Toluca in the second leg of the Apertura final.
Tijuana, coached by Argentine Antonio 'Turco' Mohamed, won 4-1 on aggregate after beating Toluca, who were looking to equal Guadalajara's record 11 titles, 2-1 at their Caliente ground on Thursday.
"This is a huge satisfaction, we've been preparing for this for six months, no one gave a cent for this team but our humility and work were reflected on the pitch today," Tijuana captain Javier Gandolfi said.
Tijuana's 'Xolos', or 'Aztec Dogs', went ahead in the 70th minute when Ruiz rammed the ball home after a shot from team-mate Fernando Arce came back off the post.
Two minutes later, in a fast counter-attack, Riascos ran onto a through ball from Ecuadorean midfielder Fidel Martinez, rounded the goalkeeper and put the tie beyond Toluca.
"I'm happy, we deserved this. We did great things, we responded to the support of the people of Tijuana with a title they'd never had," said Riascos, while thousands of fans celebrated after watching the match on giant screens at their Caliente stadium.
Guadalajara, knocked out by Toluca in the quarter-finals, ended their relationship with Dutch great Johan Cruyff, who was taken on as a consultant in February.
"Guadalajara has decided to end its contract for services and advice with Johan Cruyff's consultancy by virtue of not having achieved the results and objectives set out at the beginning," the club said in a statement.
However, it added the Chivas will continue to be coached by Dutchman John van't Schip, who was appointed by Cruyff in April.
"There will be no changes in the coaching staff since we have managed to implement a working methodology that is the basis for the successful development of the club."