The Spaniard has shown himself to be an expert at head to head battles, winning both the Saltire Energy Paul Lawrie Match Play and the Belgian Knockout, and he showed all those skills again as it came down to a three man contest at Fairmont St Andrews.
Otaegui entered the day four shots off the lead of Matt Wallace but eight birdies in 11 holes from the fifth helped him finish at 23 under, four clear of the Englishman.
Aaron Rai continued his recent excellent form to finish at 17 under, a shot clear of fellow Englishmen Chris Paisley and Garrick Porteous, with the latter challenging for the title until falling away down the stretch.
After an opening round of 62, Otaegui's 63 bookended his week beautifully and saw him get over the line after three runner up finishes in stroke play events, including this season's English Championship.
A three time Qualifying School and one time European Challenge Tour graduate, Otaegui has truly established himself on Tour since being a joint winner of the Q School in 2015, and he now has a stroke play, match play and medal match play victory on his CV.
"Stroke play is my favourite way of golf, I think it’s the proper way," he said. "You have to play very solidly and very consistently all four rounds, which I think I did. I’m very happy to be able to win stroke play as well, my third win on the European Tour.
"I had no expectations this morning, really. I just wanted to go out there, play well and shoot as well as possible. I mean, If you told me I was going to shoot 63 this morning, I wouldn’t believe it. Everything went well, I played very well, I felt very well, I was very focused and I holed some good putts. It’s been a very good week and especially today was a very good day to finish that week.
"I feel so happy. To be able to win in Scotland, especially here in St Andrews, the home of golf, it means a lot to me.
"I obviously have long term goals but I think those goals are here to make you practise better, practise harder and once you are at a tournament you just have to focus on the present. My dream has always been to win the Ryder Cup, to win Majors, but right now I’m just focused on the end of the season."
Wallace had dropped just one shot all week but his tee shot on the first ended up behind a wall and he made a bogey after chipping out sideways.
Otaegui holed a 25 footer on the first and birdied from even further out on the par three fifth but it was Porteous who soon reeled in the leader.
After both he and Wallace made the most of the short par four fourth with birdies from inside ten feet, Porteous holed an 18 footer on the fifth and made a birdie from 15 feet on the next to make it three in a row.
Otaegui was the only member of the final group to take advantage of the driveable seventh and his birdie from eight feet had him within one.
A tee shot to six feet that almost found the hole on the eighth handed him a share as Wallace made a bogey after a poor tee shot, and Otaegui led on his own at the turn as he put an approach shot to 15 feet on the ninth.
All three of the leading pack dropped shots on the tenth as Wallace needed a drop off the tee and Otaegui and Porteous failed to get up and down, but the leader extended his advantage to two with a tee shot to tap in range at the 11th.
A trio of birdies from the final group after approaches to inside ten feet followed and it truly looked like a three horse race as Otaegui holed a long putt from off the green at the 13th and Porteous made a birdie of his own from seven feet.
Porteous failed to get up and down from over the back of the 14th and Otaegui led by three, before he and Poretous both birdied the next after getting inside six feet.
Porteous then double bogeyed the 16th after leaving his second shot in the rough and dropped another on the next, with Wallace moving into second after a tee shot to seven feet on the 17th handed him a 71.
Otaegui played it safe down the last but was still able to claim a tenth birdie of the day thanks to a beautiful third.
Porteous' late slip saw him sign for a 71 and allowed Rai to take third after a bogey free 66 with gains on the first, third, fourth, seventh, 12th and last.