DOHA, 24 Jan, 2015 (AFP) - Grace became the fourth South African to win the $2.5 million tournament, following Darren Fichardt (2003), Ernie Els (2005) and Retief Goosen (2007).
After a close battle for most part of the day, Grace landed an eagle on the 16th hole to momentarily edge clear of the field but could only manage a par on the 17th, which Warren birdied to draw level.
But with the final hole remaining, Grace almost produced another eagle, getting within three feet for his fourth birdie to log a final round of 66.
That gave him an aggregate of 19-under-par 269 and the title as Warren could only par the final hole after missing the fairway and landing in the rough.
Austrian Bernd Wiesberger, who was part of a quartet who shared the overnight lead, was third with 271, while England's Eddie Pepperell was fourth on 272.
For the second consecutive day Grace produced the shot of the round – a drive to five feet on the par four 16th setting up a decisive eagle.
On Friday he had produced a miraculous wedge shot from the trees at the fifth where the resulting birdie set up a third round 68 after a shaky start.
"It was a great day, a great week, and it's another trophy to put in the cupboard," said Grace.
"This is one of the trophies you want to win," he said.
"I'm going to thank Callaway again – that driver again on 16 to four feet; without that it wouldn’t be possible.
"That wedge on the fifth hole, that was a shot that you want to hit but you don't always manage it.
"The form has been there, I played great and I managed to get in on top."
The 26-year-old also maintained his 100 percent record of winning all of his six European Tour events when leading or sharing the lead going into the final round.
All four of his previous titles came in 2012 after which he endured a two-year drought before his second win in four starts this season which could help him win a ticket to the Masters in Augusta.
Warren gave Grace a tough fight but saw his round blemished by a bogey and a double bogey over the front nine, which eventually put paid to his hopes of winning his fourth European Tour title.
"I started birdie-birdie, but it didn't feel as in-sync as it has been, and obviously starting with two birdies, you can't complain," said Warren.
"It was a little bit all over the place though, and then I hit a poor shot on eight and made double bogey there.
"Walking to the ninth tee I just thought about some swing thoughts, and moved the ball further forward in my stance for the last nine holes and never missed a shot after, so it seemed to work.
"Branden made that great eagle and then I made a good birdie on 17 just to hang on to his coat-tails a little bit. He then birdied 18 and I thought I had hit a really good drive down there to give myself a good chance at it.
"My wedge (third shot) didn't go quite as far as I thought it was going to, so it left an uphill chance to get in a playoff, and I decided to take a little break off it, so was hitting it harder than I normally would.
"I wish next week started tomorrow, after playing a final ten holes like that. It's a second place but it's not like I have made any mistakes coming in, and it was exactly the opposite to be honest."
The European Tour's 'Gulf Swing' now moves to the UAE next week for the Dubai Desert Classic.
Leading scores in Doha on Saturday after the final round of the Qatar Masters:
269 - Branden Grace (RSA) 67-68-68-66
270 - Marc Warren (SCO) 71-65-67-67
271 - Bernd Wiesberger (AUT) 69-66-68-68
272 - Eddie Pepperell (ENG) 69-71-65-67
273 - An Byeong-Hun (KOR) 67-69-72-65, Emiliano Grillo (ARG) 67-69-67-70, Grégory Bourdy (FRA) 70-68-70-65
274 - Alejandro Cañizares (ESP) 67-70-68-69
275 - Alexander Norén (SWE) 67-71-72-65
276 - Oliver Fisher (ENG) 65-73-69-69, Benjamin Hébert (FRA) 72-68-69-67
277 - George Coetzee (RSA) 68-67-70-72
278 - Justin Rose (ENG) 68-73-69-68, Henrik Stenson (SWE) 70-71-71-66, Magnus Carlsson (SWE) 71-69-70-68, Johan Carlsson (SWE) 74-65-69-70, Soren Kjeldsen (DEN) 73-70-67-68, Nicolas Colsaerts (BEL) 70-73-67-68
279 - Anders Hansen (DEN) 71-69-70-69, Julien Quesne (FRA) 70-72-69-68, Andy Sullivan (ENG) 71-68-70-70, Seve Benson (ENG) 70-71-69-69
280 - Tommy Fleetwood (ENG) 73-65-74-68, Matthew Baldwin (ENG) 70-68-70-72, Thongchai Jaidee (THA) 69-73-69-69, Ernie Els (RSA) 67-72-70-71, Darren Fichardt (RSA) 67-70-71-72, Felipe Aguilar (CHI) 71-68-72-69, Álvaro Quirós (ESP) 70-70-72-68
281 - Ricardo González (ARG) 69-70-73-69, Michaël Lorenzo-Vera (FRA) 70-70-69-72, Ross Fisher (ENG) 70-70-73-68
282 - Kristoffer Broberg (SWE) 67-71-72-72, Edoardo Molinari (ITA) 71-70-70-71, Pablo Larrazábal (ESP) 71-71-67-73, Rafael Cabrera (ESP) 66-73-70-73, Stephen Gallacher (SCO) 68-75-72-67
283 - Thomas Pieters (BEL) 73-68-68-74, Brett Rumford (AUS) 69-72-73-69, Richard Green (AUS) 70-67-76-70, Renato Paratore (ITA) 69-69-70-75, Shiv Kapur (IND) 70-68-72-73, Jeev Milkha Singh (IND) 70-70-73-70, Thomas Aiken (RSA) 69-73-72-69, Kiradech Aphibarnrat (THA) 68-71-75-69
284 - James Morrison (ENG) 68-70-75-71, Dawie Van der Walt (RSA) 72-69-70-73, Peter Lawrie (IRL) 70-68-73-73, Sergio García (ESP) 69-69-77-69, Maximilian Kieffer (GER) 71-68-73-72, Paul Lawrie (SCO) 67-73-73-71
285 - Michael Hoey (NIR) 71-69-74-71, Edouard Espana (FRA) 70-73-70-72, Mark Foster (ENG) 67-73-70-75, Andrew Johnston (ENG) 69-73-72-71, Tom Lewis (ENG) 72-71-69-73, Jason Barnes (ENG) 72-70-72-71
286 - Peter Uihlein (USA) 69-73-71-73, Damien McGrane (IRL) 68-72-74-72, Grégory Havret (FRA) 70-69-75-72, Eduardo De La Riva (ESP) 70-69-72-75
287 - Jorge Campillo (ESP) 72-70-73-72, Mark Tullo (CHI) 69-74-73-71, Robert Karlsson (SWE) 70-73-73-71
288 - Jake Roos (RSA) 75-68-72-73, Moritz Lampert (GER) 67-74-77-70, Scott Jamieson (SCO) 68-73-72-75
289 - Adrián Otaegui (ESP) 73-70-73-73, Matthew Nixon (ENG) 72-71-74-72
290 - Richard Finch (ENG) 71-72-75-72, Paul Waring (ENG) 70-72-76-72
293 - Matthew Fitzpatrick (ENG) 68-71-77-77, Wade Ormsby (AUS) 74-69-71-79
294 - Mikko Korhonen (FIN) 73-70-77-74