The 23-year-old American, who began the day two shots back of overnight leader Dustin Johnson, shot a bogey-free six-under-par 64 to reach 13 under for the tournament.
Former world number one Johnson (68) and English Ryder Cup veteran Paul Casey (66) finished in a share of second place.
"It's amazing, it's been a life goal," Morikawa said after receiving the trophy. "But to close it out here in San Francisco, pretty much my second home, is pretty special."
The first major of the COVID-19 era looked headed for a playoff as the day began with 11 players within three shots of Johnson, and at one point late in the round seven players held a share of first place.
Morikawa seized the outright lead at the par-four 14th where he chipped in from 54 feet for birdie.
Then, after narrowly missing at birdie at 15, Morikawa hit the shot of the tournament as his tee shot at the 294-yard par-four 16th hole settled seven feet from the cup for an eagle that sent him on his way.
With the win, Morikawa joins Jack Nicklaus, Tiger Woods and Rory McIlroy as the only players since World War 2 to win the PGA Championship at age 23 or younger.
Scores
-13 Collin Morikawa (USA) 69 69 65 64
-11 Paul Casey (England) 68 67 68 66
Dustin Johnson (USA) 69 67 65 68
-10 Jason Day (Australia) 65 69 70 66
Bryson DeChambeau (USA) 68 70 66 66
Tony Finau (USA) 67 70 67 66
Scottie Scheffler (USA) 66 71 65 68
Matthew Wolff (USA) 69 68 68 65
-9 Justin Rose (England) 66 68 70 67
-8 Cameron Champ (USA) 71 64 67 70
Joel Dahmen (USA) 69 68 68 67
Xander Schauffele (USA) 66 70 69 67
-7 Daniel Berger (USA) 67 67 70 69
Si Woo Kim (Korea Republic) 69 68 68 68
Jon Rahm (Spain) 70 69 68 66
Patrick Reed (USA) 68 70 69 66
-6 HaoTong Li (China PR) 67 65 73 69
Brendon Todd (USA) 65 70 72 67
-5 Harris English (USA) 69 71 69 66
Lanto Griffin (USA) 68 68 71 68
Kevin Kisner (USA) 67 73 68 67
-4 Byeong Hun An (Korea Republic) 72 69 71 64
Hideki Matsuyama (Japan) 70 67 69 70
Alex Noren (Sweden) 67 69 73 67
Victor Perez (France) 70 69 69 68
Ian Poulter (England) 73 68 66 69
Adam Scott (Australia) 68 70 70 68
Brendan Steele (USA) 66 71 72 67
-3 Tommy Fleetwood (England) 70 64 70 73
Brooks Koepka (USA) 66 68 69 74
Doc Redman (USA) 73 67 70 67
Harold Varner III (USA) 72 66 69 70
-2 Dylan Frittelli (South Africa) 70 67 70 71
Viktor Hovland (Norway) 68 71 73 66
Rory McIlroy (Northern Ireland) 70 69 71 68
Louis Oosthuizen (South Africa) 70 71 70 67
-1 Bud Cauley (USA) 66 71 73 69
Russell Henley (USA) 71 69 71 68
Nate Lashley (USA) 69 70 70 70
Webb Simpson (USA) 71 68 68 72
Justin Thomas (USA) 71 70 68 70
Tiger Woods (USA) 68 72 72 67
0 Abraham Ancer (Mexico) 69 70 72 69
Patrick Cantlay (USA) 73 68 66 73
Billy Horschel (USA) 69 71 71 69
Mike Lorenzo-Vera (France) 66 68 72 74
Keith Mitchell (USA) 68 72 68 72
Ryan Palmer (USA) 74 66 76 64
Cameron Smith (Australia) 71 69 70 70
Bernd Wiesberger (Austria) 68 68 70 74
1 Mark Hubbard (USA) 70 71 70 70
Kurt Kitayama (USA) 68 72 70 71
Luke List (USA) 72 69 70 70
Adam Long (USA) 73 68 72 68
Joost Luiten (Netherlands) 71 68 73 69
Brandt Snedeker (USA) 72 66 72 71
Erik Van Rooyen (South Africa) 71 70 74 66
2 Adam Hadwin (Canada) 68 71 70 73
Brian Harman (USA) 68 71 71 72
Tom Hoge (USA) 72 68 72 70
Mackenzie Hughes (Canada) 73 68 69 72
Denny McCarthy (USA) 70 69 70 73
Charl Schwartzel (South Africa) 73 68 68 73
Kevin Streelman (USA) 69 70 73 70
Gary Woodland (USA) 67 72 73 70
3 Emiliano Grillo (Argentina) 70 70 70 73
Shane Lowry (Republic of Ireland) 68 72 69 74
Robert MacIntyre (Scotland) 73 67 74 69
Rory Sabbatini (South Africa) 71 70 72 70
Sepp Straka (Austria) 70 71 71 71
4 Danny Lee (New Zealand) 69 71 74 70
Phil Mickelson (USA) 72 69 70 73
Jordan Spieth (USA) 73 68 76 67
Bubba Watson (USA) 70 71 73 70
6 J.T. Poston (USA) 67 74 75 70
Chez Reavie (USA) 71 75 70
7 Jim Herman (USA) 71 69 72 75
Matt Wallace (England) 71 70 74 72
10 Sung-hoon Kang (Korea Republic) 70 71 76 73
