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Watney, who finished second at Doral two years ago, birdied the 18th to make sure of victory with a five-under-par round of 67, securing his third PGA Tour win.
"This means so much, it is the biggest day of my golfing career," said Watney, who in 2009 was in contention until the final hole before losing to Phil Mickelson. "With the way it ended two years ago ... I'm very proud."
Johnson had eased the pressure on Watney with a bogey on the 16th but the winner showed his steel with an aggressive approach to the final hole where he found water on Saturday.
"The tournament wasn't over and I wanted to give myself a putt. I putted the best I've ever putted under pressure today and it worked out," said Watney.
Dane Anders Hansen and Italian Francesco Molinari were tied for third place while Britain's Luke Donald, who began the day two shots off the lead, had to settle for a share of sixth place with Australian Adam Scott.
Watney's putting was particularly impressive with him saving par with long efforts on the par three 13th and 15th holes.
"I feel like that is what happens when you win a golf tournament – you make some putts that you need to," he said.
World No 1 Martin Kaymer had a disappointing day, fading out of contention with three bogeys before slumping to a tie for 24th after finding the water on the 18th and making a double bogey.
Tiger Woods equalled the best round of the day with a six-under-par 66, earning him his first top-10 finish in a PGA Tour event since the US Open in June.
Woods's performance will give him a real boost ahead of his final pre-Masters tournament at Bay Hill later this month.
"It's definitely getting better, there's no doubt. I'm putting the pieces together. Everything is kind of shaping up and heading in the right direction and peaking at the right time," said Woods.
American Rickie Fowler offered a reminder of his promise, the 22-year-old shooting Sunday's other 66, to finish eighth.
World No 2 Lee Westwood enjoyed a good final round, shooting a four under 68 to finish tied for 18th but Northern Ireland's Rory McIlroy, who found water on the final hole, will be disappointed with his two-over-par final round.
Leading final scores here on Sunday in the $8.75 million World Golf Championships Cadillac Championship (USA unless noted, par-72 course):
272 - Nick Watney 67-70-68-67
274 - Dustin Johnson 69-69-65-71
275 - Anders Hansen (DEN) 71-69-68-67, Francesco Molinari (ITA) 68-68-70-69
276 - Matt Kuchar 68-69-68-71
277 - Luke Donald (GBR) 67-72-66-72, Adam Scott (AUS) 68-70-68-71
278 - Rickie Fowler 71-73-68-66
279 - Hunter Mahan 64-71-71-73
280 - Jonathan Byrd 70-74-68-68, Padraig Harrington (IRL) 68-71-68-73, Martin Laird (GBR) 67-70-70-73, Rory McIlroy (NIR) 68-69-69-74, Tiger Woods 70-74-70-66
281 - Robert Allenby (AUS) 72-72-69-68, Ernie Els (RSA) 69-70-73-69, Kevin Streelman 68-72-72-69
282 - Paul Casey (GBR) 70-71-69-72, Louis Oosthuizen (RSA) 71-73-67-71, Steve Stricker 68-71-69-74, Lee Westwood (GBR) 70-74-70-68
...
283 - Vijay Singh (FIJ) 68-72-68-75
284 - Martin Kaymer (GER) 66-70-74-74, Charl Schwartzel (RSA) 71-71-75-67
285 - Aaron Baddeley (AUS) 72-66-73-74, Thomas Bjorn (DEN) 71-73-70-71, Rory Sabbatini (RSA) 74-74-67-70
286 - Retief Goosen (RSA) 69-76-68-73, Robert Karlsson (SWE) 69-73-71-73, Jhonattan Vegas (VEN) 69-74-69-74
287 - Camilo Villegas (COL) 71-71-73-72, Thomas Aiken (RSA) 68-75-74-70
288 - K.J. Choi (KOR) 73-69-72-74, Edoardo Molinari (ITA) 71-73-70-74, Yong-eun Yang (KOR) 73-72-72-71
289 - Ryo Ishikawa (JPN) 65-76-70-78, Graeme McDowell (NIR) 70-73-71-75, Justin Rose (GBR) 77-71-70-71
290 - Jason Day (AUS) 71-76-71-72, Marcus Fraser (AUS) 69-78-71-72
Ian Poulter (GBR) 73-70-74-73
291 - S.S.P. Chowrasia (IND) 74-72-72-73, Kyung-tae Kim (KOR) 73-70-73-75, Geoff Ogilvy (AUS) 76-73-72-70
292 - Peter Hanson (SWE) 73-73-73-73, Yuta Ikeda (JPN) 74-73-74-71, Miguel Angel Jimenez (ESP) 71-72-73-76, Phil Mickelson 73-71-72-76
293 - Seung-yul Noh (KOR) 72-70-79-72
295 - Rhys Davies (GBR) 73-76-72-74, Ross Fisher (GBR) 69-76-76-74, Hiroyuki Fujita (JPN) 71-73-74-77
296 - Alvaro Quiros (ESP) 70-77-74-75, Peter Senior (AUS) 75-73-73-75
