Warren holed a birdie putt on the 18th at Gleneagles to finish with a 69 and get into a playoff with Wakefield, who shot a 70. Both finished at 12-under 280.
In the playoff, both got pars on the first hole. On the second, Warren set up his birdie with a putt from 60 feet that stopped within five feet of the cup.
The victory was the 25-year-old Scot's second on the European Tour. Both have come on the second playoff hole.
Martin Erlandsson (66) and Soren Hansen (68) shared third place, one shot behind. Erlandsson had two eagles on the front nine.
Hansen missed the playoff when he failed to make a six-foot birdie putt on the last hole.
Fredrik Andersson (72), who led with Wakefield overnight, shared fifth place with Graeme Storm (69).