France's Mattieu Pavon finished third on 10 under after a final-round 66, a position that also qualifies him for Birkdale along with Australia's Andrew Dodt, who gets his first shot at a major.
Shinkwin had looked set for his maiden European Tour title only to fluff his chip to the 18th in regulation and then leave a putt to win the short from just 1.2 metres.
The Australian held a share of the lead as he entered the final round, and despite carding a one-over-par 73, managed to snatch one of three places on offer to golf's oldest major. Cabrera Bello eventually defeated Shinkwin in a playoff.
Shinkwin, looking for his first European Tour victory, stood on the 18 tee with a one-shot advantage over Cabrera Bello, but pushed his approach shot left of the green on the par-five and was left with a tricky third shot over a bunker.
"I'm extremely happy", said Cabrera-Bello.
"I feel that I played some of the best golf of my life today".
Padraig Harrington, Anthony Wall, Matt Kuchar and Ryan Fox shared fourth place with Andrew Dodt at eight-under, while Rickie Fowler, Soren Kjeldsen, Lee Slattery, Andy Sullivan and Robert Rock made up the rest of the top 10 in a tie for ninth with Ian Poulter at 7-under. "It wasn't there for me", Shinkwin said. "Sometimes I did mistakes, sometimes it didn't work out for me". "I think that was a valuable experience, precious experience for me". It's possible looking at the forecast and although yesterday wasn't very enjoyable, it was nice to see my driver got 230 yards off the tee and my 2-iron go 180 yards.
The result is Dodt's sixth top-0o in his 26 Tour events this year and, in some way, makes amends for last May's disappointment in leading going into the final round of the BMW PGA Championship but only to finish in a share of sixth on the famed "Burma Road" course. But it's all a learning curve and obviously if you win, you have to have luck on your side. "Now I've got enough ranking points to hopefully be in The Race to Dubai at the end of the year and hopefully I can carry on into next week". "I played great yesterday and today. That birdie made my day".
The 2013 Masters champion closed with a four-under-par 68 at Dundonald Links to finish three-under-par overall in what was his first Scottish Open appearance since 2009.
The 30-year-old then struggled on the 18th par five in which he'd hit an eagle in the first round followed by two birdies on previous days, registering a par.