South African-born Gonzalez headed down a cross from substitute Esteban Paredes in the 75th minute to break the deadlock in a match where the stubborn Swiss set a World Cup record of 558 minutes without conceding a goal.
GEAR:Get a Jabulani ball
Chile never gave up and bombarded the Swiss goal, stepping up a gear after Switzerland had Valon Behrami sent off in the 31st minute for violent conduct in an ill-tempered match full of tough tackles, free kicks and colourful Chilean dives.
The draw left Chile top on six points followed by Switzerland on three then Spain and Honduras, who are both without a point and play later on Monday in Johannesburg.
LIVE:Minute-by-minute coverage
"We had lots of opportunities to score one goal and had the advantage of playing with one more player," Chile's Argentine coach Marcello Bielsa said with a stern face and his trademark deadpan delivery.
"Football is a game that brings the unexpected results. We're not yet qualified and we have to fight with the same enthusiasm was have had until now."
The match lived up to its billing as an ugly midfield battle, with the Swiss rarely venturing forward and opting to crowd out centre of the pitch to smother Chile's free-flowing attacks.
POTENT ATTACKS
But the Chileans, who opened their campaign with their first World Cup win in 48 years, refused to settle for a draw and piled on the pressure, with the pacy Alexis Sanchez instrumental in nearly all of Chile's potent attacks.
Chile recalled Humberto Suazo, the top scorer in South American qualifying, but his halftime replacement Gonzalez was far more effective and proved too hot for the Swiss to handle.
Chile rushed forward right from the start but were frustrated by the tight-marking Swiss, but their defence slowly started to come undone after the half hour mark when Behrami was adjudged to have elbowed Arturo Vidal, who slumped theatrically to the ground clutching his face.
"The World Cup was a dream for me and I'm disappointed by the red card," Behrami said. "The television images speak for themselves. I was just defending but Vidal is a great actor."
Chile thought they had broke the deadlock soon after the break when Sanchez's strike from 25 metres deflected off Matias Fernandez and into the net but was ruled out for offside.
They almost found their goal on 54 minutes when Sanchez dispossessed Stephane Grichting on the edge of the area but was denied by Benaglio for the third time in the match.
But it was the two substitutes that made the difference, with Paredes breaking clear and whipping a neat cross over the stranded Benaglio onto the path of Gonazlez, who found the net from six metres.
Switzerland's German coach Ottmar Hi
