The Spaniard entered the final day in California three shots off the lead but enjoyed a birdie birdie start as a host of the game's biggest names made moves on a dramatic afternoon in California.
But as everyone else fell back, it came down to a two horse race between Rahm and Louis Oosthuizen, with the South African holding a one shot advantage as his rival stood on the 17th tee.
Rahm then produced a finish that will go down in Major history, making a pair of birdies on his final two holes to sign for a 67 and walk off the 18th green with a one shot lead at six under and his son Kepa in his arms on his first United States Father's Day.
Oosthuizen found a hazard off the tee on the 17th and the resulting bogey meant he needed an eagle up the last for a play-off, with the 2010 Open Champion making a birdie in a closing 71 that left him at five under and second in a Major for the sixth time.
Rahm's win moves him to Number One in the Race to Dubai Rankings in Partnership with Rolex and the Official World Golf Ranking and comes at the scene of his first professional win at the Wells Fargo Championship on the US PGA Tour four years ago.
It also arrives just two weeks after he tested positive for Covid-19 and was withdrawn from the Memorial Tournament while holding a six shot lead after three rounds, and he revealed that Padraig Harrington and Sir Nick Faldo had both offered their support after that disappointment.
“I’m a big believer in karma and after what happened a couple of weeks ago I stayed really positive, knowing big things were coming,” he said.
“I didn’t know what it was going to be but I knew we were coming to a special place, I knew I got my breakthrough win here and it’s a very special place for my family.
“The fact my parents were able to come, I got out of Covid protocol early, I just felt like the stars were aligning.
"It felt like such a fairy tale story that I knew it was going to have a happy ending. I could just tell, just going down the fairway after that first tee shot, that second shot, and that birdie I knew there was something special in the air. I could just feel it. I just knew it.
"I couldn't have told you in the moment I felt something special. That's why I played as aggressive as I did because it was like, 'man, this is my day; everything's going to go right'. I felt like that helped me become. I just knew that I could do it and believed it."
"This was definitely for Seve," he added. "I know he tried a lot and usually we think a lot about him with the Masters but I know he wanted to win this one most of all."
Rahm made a fast start by taking a brave line at the first and holing from ten feet and then leaving himself a flick to three feet at the second.
This was definitely for Seve. I know he tried a lot and usually we think a lot about him with the Masters but I know he wanted to win this one most of all
A bogey after finding a bunker off the fourth tee dropped him back but he got a fortunate bounce at the ninth when his wayward tee shot was stopped from going out of bounds by a temporary fence. From the resulting free drop he played out to 105 yards and got up and down to move to four under.
The leaderboard had tightened up in the early stages but after putting an approach to four feet at the fifth, defending champion Bryson DeChambeau was an inch from a hole-in-one at the eighth and out in front on his own at five under.
Oosthuizen had found sand off the tee at the fourth to drop a shot but he laid up at the ninth and then holed from 16 feet to join DeChambeau before holing from nearly 30 feet at the tenth to take the lead on his own.
DeChambeau missed the green after failing to get up and down on the 11th but Oosthuizen's two shot lead did not last long as he did the same after finding a similar spot.
It was back to back bogeys for DeChambeau as he found some very heavy rough on the 12th and Rahm was now Oosthuizen's nearest challenger, with the American eventually finishing at three over as he came home in 44.
Rahm had started the back nine with seven birdies in a row but he broke that run with a brilliant 25 foot left to righter on the 17th which brought a fist pumping celebration.
A bigger moment and a bigger celebration was to come, however, as he found sand with his second on the last but played a treacherous bunker shot brilliantly and holed another left to righter from 18 feet to set the target.
Oosthuizen's bogey on the 17th left him with a mountain to climb and he could only lay up after finding rough off the tee at the 18th and signed for a 71 with a closing birdie.
English and Migliozzi - whose top four finish earns him a place at the 2022 Masters Tournament - both signed for rounds of 68, with Koepka recording a 69 and Morikawa a 70.