The 24-year-old claimed his second victory in Madrid as he closed with a blemish-free five-under 66 for a 19-under 265 total at the Club de Campo de Madrid.
Schwartzel, whose previous Madrid win was in last year's Spanish Open, went into the final round a stroke better than Gonzalez and never let the burly Argentine get on terms.
Spain's Pablo Larrazabal began the day three shots behind Schwartzel and he, too, had no answer to the young South African's serene display and finished third four strokes behind the winner.
Two front-nine birdies and three more in five holes from the 13th saw Schwartzel maintain a commanding lead and earned him the £135,000 first prize.
Schwartzel had been so troubled by a respiratory infection and a sore shoulder-blade before his round on Friday he was on the point of pulling out of the tournament.
His father George advised him to play on, via a telephone call home, and see how he went. Schwartzel responded with a 64 to hit the front in Madrid and was never headed.
"I'm really glad I took his advice," Schwartzel said. "It will take a lot for me not to want to play but I was down on my energy and very sore when I woke up in the morning.
"This morning, though, I felt fine. But I played really well for the whole week. I'm looking forward to next season on the European Tour because it's going to be a big one," he added.
Gonzalez's putter in his final round 68 was never as hot as it was in the third round when he needed only 10 putts in a back-nine 27 when posting a 62 that put him in contention.
When the Argentine bogeyed the 13th he found himself with too much to do to follow up his Madrid Open victory on the same course in 2003.
Larrazabal's 67 helped rubber-stamp his claim to the European Tour rookie of the year award.
Two-times Masters champion Jose Maria Olazabal tied for 65th on two-over after closing with a 73 but he was happy with his return from a three-month lay-off through injury and illness.
"The best thing about the week was that the back held up and I didn't feel a lot of tightness," he said.