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Johnson captured his sixth US PGA victory at the $5.6 million event, his first since last year's Barclays, by firing a final-round 66, four-under par, that included birdies at the par-5 16th and par-4 17th holes.
Johnson finished 72 holes on nine-under par 271, one stroke ahead of fellow American John Merrick and two in front of Australian Nick O'Hern and Americans Davis Love, Ryan Palmer and Chad Campbell.
Northern Ireland's McIlroy, who defends his US Open crown starting on Thursday at The Olympic Club, was among half a dozen contenders within a stroke of the lead over the final holes at TPC Southwind.
McIlroy birdied the par-4 second, par-3 fourth and par-4 seventh holes and added another at the par-3 11th to put himself in the title hunt. Even after bogeys at the par-4 12th and par-3 14th he was among the leaders.
A birdie at the par-4 17th gave him a share of the lead at eight-under, but McIlroy's double bogey at 18 left him with a 69 to share seventh on 274 with American Ken Duke, Australian Robert Allenby and South Korean Seung-Yul Noh.
Johnson started well with an opening birdie and back-to-back birdies at the sixth and seventh before closing the front nine with his lone bogey of the day, then making six pars before his back-to-back bogeys and a closing par to win.
Merrick birdied the 15th an 16th but was undone by his double bogey at 12 while Campbell and O'Hern were undone by bogeys at 18.
271 - Dustin Johnson 70-68-67-66
272 - John Merrick 66-69-69-68
273 - Ryan Palmer 74-66-67-66, Chad Campbell 68-67-70-68, Nick O'Hern (AUS) 70-67-67-69, Davis Love 68-68-68-69
274 - Ken Duke 68-68-73-65, Seung-yul Noh (KOR) 67-69-72-66, Rory McIlroy (NIR) 68-65-72-69, Robert Allenby (AUS) 68-70-67-69
275 - Greg Owen (ENG) 72-67-71-65, Kevin Stadler 69-65-71-70
276 - Martin Flores 72-70-69-65, William McGirt 71-69-68-68, Henrik Stenson (SWE) 72-66-70-68, Jeff Overton 67-72-68-69, Padraig Harrington (IRL) 68-68-71-69, Kevin Kisner 69-66-70-71
277 - Arjun Atwal (IND) 67-74-70-66, Woody Austin 72-68-67-70, Luke Guthrie 69-71-67-70, John Daly 68-69-76-64, J.B. Holmes 70-64-72-71
278 - Duffy Waldorf 71-69-69-69, Bryce Molder 69-71-69-69, Martin Laird (SCO) 72-70-67-69
