However Gonzalez stalled the charge, taking the second set to a tie-breaker where Federer suffered an uncharacteristic implosion, fluffing an overhead and playing a panicky lob.
In the deciding set, Federer staved off break points in the third and fifth games but was broken for the first time for 6-5 as Gonzalez hammered ground strokes before finishing with a deft volley.
Gonzalez, who had saved five break points of his own, raced to 40-0 in the next game and celebrated a famous victory as Federer hooked a forehand wide.
"Nobody beats me 11 times in a row!" said the jubilant Chilean.
"Of course he was the favourite. I had a lot of motivation, I was really excited when I went to the court.
"I think he played the first five games like a real number one. But after that he went down a little bit and my level went up. I think the key to the match was my serve and not being scared to go for my shots."
The South American's heroics add unexpected spice to the Masters Cup, where Federer was the overwhelming favourite for his fourth title.
The 26-year-old Federer won the Masters in 2003, 2004 and 2006, falling to Lleyton Hewitt in the 2002 semis and losing a marathon final to Nalbandian in 2005.
Gonzalez, 27, is making his second appearance at the tournament after playing as an alternate in 2005, when he failed to reach the knock-outs.
In Red Group's earlier match, troubled Russian Nikolay Davydenko's horror season continued when he was hammered by racquet-breaking Andy Roddick.
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