Fleetwood also birdied the 18th to finish his round with a 70 and set up a three-way playoff with Scotland's Stephen Gallacher (67) and Argentina's Ricardo Gonzalez (70) after all three finished on 18-under 270 on the PGA Centenary course.
Playing the par-5 18th again, Fleetwood narrowly missed an eagle putt from the fringe and then rolled in a three-footer for the win. Gallacher and Gonzalez both made par.
Gallacher overcame a triple-bogey 7 on the 11th hole with a round that included five birdies and two eagles — including one on the 18th to make the playoff.
Collated leading final round scores in the Johnnie Walker Championship at Gleneagles on Sunday (GBR and IRL unless stated, par 72):
270 - Tommy Fleetwood 68 65 67 70 (Tommy Fleetwood won at 1st playoff hole), Ricardo Gonzalez (ARG) 65 65 70 70, Stephen Gallacher 71 68 64 67
271 - Scott Henry 72 65 67 67, Bernd Wiesberger (AUT) 65 66 72 68
272 - Brett Rumford (AUS) 66 69 69 68, Emiliano Grillo (ARG) 71 66 69 66, Paul Waring 75 63 67 67
273 - Thorbjorn Olesen (DEN) 71 68 66 68
274 - David Drysdale 71 67 68 68, Richie Ramsay 69 68 69 68, Shane Lowry 68 70 67 69, Mikko Korhonen (FIN) 71 69 67 67
275 - Craig Lee 69 67 71 68, David Horsey 70 68 69 68, Morten Orum Madsen (DEN) 70 70 67 68
276 - Gary Boyd 71 69 68 68, Ross Fisher 66 72 66 72, Anders Hansen (DEN) 70 69 68 69, David Howell 71 70 67 68, Tom Lewis 67 71 67 71, Thongchai Jaidee (THA) 66 69 73 68
277 - John Parry 71 66 70 70, Richard Finch 73 67 68 69, Espen Kofstad (NOR) 71 70 68 68, Gregory Bourdy (FRA) 68 71 70 68, Fredrik Andersson Hed (SWE) 68 67 66 76