Tijuana, which was only founded in 2007, claimed the two-legged final 4-1 on aggregate after a 2-1 home win last week.
Toluca was attempting to win its 11th league title to equal Guadalajara Chivas as the country's most successful club.
Ruiz opened the scoring with a tap in from close range in the 70th minute, after a free kick on the edge of the area rebounded off the post and into his path.
Riascos took a pass, rounded goalkeeper Alfredo Talavera and finished into an empty net two minutes later to leave Toluca needing three goals.
"This team deserves it. We've never complained about the traveling or anything," Tijuana-born midfielder Fernando Arce said. "We're champions, we're at the top and we'll enjoy it."
Tijuana often traveled vast distances to play its away matches, including more than 2,000 kilometers (1,250 miles) to Toluca.
Prior to Tijuana's breakthrough, the game was a scrappy affair with few genuine opportunities, as Toluca showed little of the flair that saw it finish top of the regular season table.
United States international Edgar Castillo came close for Tijuana in the 49th when he rifled a left footed strike toward the top left corner of the net, before Talavera tipped it over.
Toluca's best chance was in the 57th when Panama's Luis Tejada headed over from three yards after Lucas Silva had knocked the ball back across goal.
In the first leg on Thursday, Paul Aguilar and Fidel Martinez got the goals for Tijuana, with Edgar Benitez scoring for Toluca.
The team from the Mexico-United States border has brought together a city that has had a reputation for drug-related violence.
The popularity of the team has aided the city in improving its image after years of negative headlines.
The club's nickname is "Los Xolos," short for Xoloitzcuintles, a type of dog indigenous to Mexico in the Azteca times.
Tijuana has also gained supporters in the United States by using English on its social networking sites and playing with American born players Joe Corona, Castillo and Greg Garza. Corona and Castillo are regulars in U.S. squads.
The club also fielded six players born in South America for the final, with only three of its players actually born in Mexico.
"I dedicate the win to all the players and the people that have stuck with me," Tijuana coach Antonio Mohamed said.
Like most Latin American countries, Mexico plays a split season and crowns two champions each year. The Apertura title is followed by the Clausura competition in the first half of 2013.
Extra note to possibly add: It's almost 2,000 kilometers to Tijuana's nearest away game - in Torreon to face Santos Laguna - and many Mexican teams are situated in cities at altitude, making it especially difficult for the club to win the title.
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