Australia's long history of heartache at Augusta National continued as Schwartzel birdied the last four holes to shoot a six-under-par 66 closing round and win by two strokes from debutant Day (68) and fellow Queenslander Scott (67) at 14-under 274.
Wielding his broomstick putter with rare certainty Scott led by two strokes with two holes left but, despite parring home, was unable to hold off the fast-finishing Schwartzel.
Schwartzel becomes the third South African to win the green jacket after Gary Player and Trevor Immelman.
Another Australian, Geoff Ogilvy, fired a 67 to finish four shots behind in a tie for fourth with Tiger Woods (67) and Englishman Luke Donald.
Scott and Day played together in the third last group and fed off each other's good play.
"To be right in the mix is everything I've dreamed of. It just didn't pan out," said Scott.
"I've got to be pretty proud of the way I played over the weekend. Obviously I can't control Charl.
"When you birdie the last four holes at the Masters when you're around the lead, that usually wins.
"I'm disappointed I didn't win when I held the lead with a few holes to go. It's exciting to be in the mix at a major, something I haven't been able to talk about before.
"It would have made the Masters exciting for (Australian golf fans) to have three guys contending on the back nine on Sunday. It's been a while."
The 23-year-old Day could hardly have been more impressive in his first appearance in the Masters and he charged home with birdies at the last two holes.
"I couldn't do any more than what I did today. Adam and I played wonderful golf and Charl played even better golf," said Day.
"I've known Adam since I was 15. We've been good mates since then. We had a lot of fun today.
"It was really really good to be in the hunt for the Masters."
Third round leader Rory McIlroy collapsed with an 80 to finish equal 15th.
