Both players shot 1-under 70 in the final round, each parring the final six holes to finish at 5-under 279. In the playoff, Van der Walt of South Africa bogeyed No. 18 while Thornton made a short par putt to win the title.
Seve Benson of England shot 70 to finish third, one stroke back. Englishman
"I've been working hard on my short game for a couple of years now so I'm delighted," Thornton said. "I changed my putter and my putting technique last week too, so it all came together this week."
Thornton finished tied for 11th at this tournament last year. His only other top-10 finish on the European Tour was ninth at the BMW International Open in Munich in 2010.
The tearful Irishman dedicated the victory to his deceased father.
"It's so big for me," Thornton said. "On Father's Day, too. He passed away three years ago and it still hurts. But they are happy tears today. This is dedicated to him."
Thornton, Van der Walt and Frenchman
Van der Walt and Thornton swapped the lead on the front nine before Benson joined the hunt for the title on the back nine.
Thornton birdied the 10th to move one stroke clear of Van der Walt. But the South African rallied by picking up a shot on the 12th.
Benson hit two straight birdies to draw level atop the leaderboard but faded when he bogeyed the 16th.
"It's really disappointing to get so close and not finish it off," said Van der Walt, the runner-up at the Africa Open last year.
Van der Walt led Thursday and shared the lead in the final three rounds.