Kingston defeated Anders Hansen, who missed a 6-footer for par on the extra hole, which was played in rain and near darkness.
The two players had finished regulation play at 13-under-par 275. Kingston shot a 69 and Hansen had a 67 in the final round.
The victory Kingston's second on the European Tour.
"A week ago I didn't even know I was in the event," Kingston said. "I got in through last year's rankings, so to come out and win a championship like the Mercedes-Benz Championship ... makes it more special.
Simon Dyson (70) and Peter Hanson (71) tied for third-place at 276.