Gonzalez had barely been on the pitch for a minute before he pounced on some slack defending as Chile were caught napping in the 80th minute at the Estadio Monumental David Arellano.
Both of Chile's central defenders were caught under the flight of the ball, allowing Diego Rolan to collect the ball and square for substitute midfielder Gonzalez, who made no mistake from close range.
Earlier, in-form striker Alexis Sanchez got the ball rolling, heading Chile into a 28th-minute lead.
But visitors Uruguay hit back on the stroke of half-time as young forward Rolan netted his first senior goal for his country against the run of play.
Chile made two changes to the team that routed Venezuela 5-0 on Friday, with Jorge Sampaoli drafting in Gonzalo Jara and Fabian Orellana at the expense of Igor Lichnovsky and Jorge Valdivia.
Uruguay were without talisman Luis Suarez, who was on target during Thursday's 3-3 draw with Costa Rica, after the Barcelona striker was sent back to Spain by coach Oscar Tabarez.
Rolan was named as Suarez's replacement, partnering Edinson Cavani up front.
Both teams made a lively start to proceedings and Sanchez came closest to breaking the deadlock from a free-kick in the 11th minute, but Uruguay goalkeeper Fernando Muslera was up to the task, tipping the ball over for a corner.
Chile began to assert their dominance on the match and took a 28th-minute lead courtesy of Sanchez, who continued his brilliant run of goalscoring form.
Sanchez guided his header into the bottom corner of the net from Orellana's cross for his second international goal in less than a week.
It was Sanchez's ninth goal in six games for both club and country.
Uruguay were second-best from that moment but somehow managed to go into the break on level terms after an unmarked Rolan nodded home Carlos Sanchez's perfectly executed set-piece on the stroke of half-time.
The goal came about after tenacious Chile midfielder Gary Medel gave away a free-kick on the wing and almost sparked an on-field brawl following an altercation with Cavani.
Uruguay started the second half on the front foot, providing more of a threat in the final third but it was Chile who almost regained the lead in the 57th minute after Orellana - the supplier of the opening goal - danced past his opponent and looped his cross-cum-shot effort into the post.
The match sparked into life 21 minutes from time as Chile keeper Claudio Bravo was forced into action, somehow getting a hand on the ball to deny Rolan a brace after Cristian Rodriguez whipped in a cross from the left-hand side.
A minute later, Chile thought they had scored at the other end but the linesman flagged for offside, though replays suggested it was the wrong call.
Uruguay hit the front with 10 minutes remaining, Gonzalez tucking the ball underneath Bravo after a mix up between the two Chilean central defenders.
The visitors had two chances in the closing stages to put the game to bed and missed both, but they still hung on for the win as Chile's five-game unbeaten run came to an end.
