The American started the final day a shot behind 2010 Champion Louis Oosthuizen but soon hit the front and led by four at the turn courtesy of a hat-trick of birdies from the seventh.
Countryman Jordan Spieth applied the pressure on the back nine with a skilful and dogged performance as he carded a 66 but Morikawa held his nerve to sign for a 66 of his own, a 15 under par total and a two shot victory over the 2017 Champion.
The victory makes Morikawa the first player in history to win two Majors on debut after his triumph at the 2020 US PGA Championship and he becomes the first to win two in his first eight starts since the great Bobby Jones in 1926.
The 24-year-old also makes it three wins in 14 European Tour appearances after becoming the youngest player since Seve Ballesteros in 1979 to come from behind on day four and win the Claret Jug.
"It's amazing," he said. "I tell everyone I'm not the biggest history guy but I want to add myself into history and I want to make memories for myself and to be holding the Claret Jug is one of the best memories I'm going to have in my lifetime.
"I've had belief in myself since day one that I turned professional that I can do it, not give myself time to prep but just really learn the ropes and be out here and make a statement for myself.
"When it comes to these tournaments I've never played, a golf course and style that I've never played, I do my work. Last week at the Scottish Open was a huge week of learning experience for me. I put it all together and thankfully it all paid off this week."
The final pair made a quiet start and when they both missed the green at the fourth, it was Oosthuizen who failed to get up and down and they were tied at 11 under.
There was then a two shot swing on the par five seventh as Morikawa made his birdie as he got up and down from the front of the green, with Oosthuizen going from one bunker to another around the green and dropping a shot.
To be holding the Claret Jug is one of the best memories I'm going to have in my lifetime
Spieth made a slow start and registered bogeys as he missed the green at the fourth and found sand at the sixth but he put an incredible second to around 20 feet at the seventh for an eagle and then holed a ten footer at the ninth to sit alongside Oosthuizen.
Morikawa was just getting started, however, and he hit a stunning second to four feet at the eighth and then holed from 25 feet at the ninth to make the turn with a four shot lead.
Spieth trimmed the gap to three from 15 feet at the tenth and after the leading duo made stunning up-and-downs to save par at the tenth and 12th respectively, Oosthuizen hit the flag with his tee shot at the 11th and rolled home from four feet to get back into a share of second.
A charging Spieth put his second to eight feet at the 13th and holed from six feet after laying up at the next to apply the pressure but Morikawa showed no signs of faltering, making an 18 footer up the hill on the 14th to be two ahead.
Another excellent par save on the 15th maintained his two shot advantage and he looked a picture of calm as he closed out victory, with Spieth also finishing with four pars.
Oosthuizen had dropped a shot on the 13th but bounced back with a tap-in birdie on the next to card a 71 and secure a tie for third after finishing second at the US PGA and the U.S. Open Championships on the 2021 Race to Dubai.
Rahm bogeyed the second and despite a remarkable eagle from four feet on the seventh, he was still well off the pace when he dropped a shot on the next.
But a birdie on the 13th kickstarted his round and he made another on the 14th after having a good look at eagle, holed a 20 footer on the 15th and left himself a tap-in at the 16th in a 66.