English world number 405 Shinkwin, 24, took six shots when needing a par five at the final hole for a first European Tour title, but qualifies for the Open.
Cabrera-Bello carded an eight-under course record 64 to finish the regulation 72 holes in 13 under.
Ian Poulter, the 41-year-old seeking a first title since 2012, had five bogeys in a 74 and shared ninth.
Shinkwin, from Watford, had been at the top of the leaderboard since the second round and did not drop a shot in the first 17 holes on the final day at the Dundonald Links in Ayrshire.
But he took four to get down from level with the green at the par-five 18th, leaving a seven-foot putt short. Then at the same hole in the play-off, he saw a putt from a similar spot also fail to reach the cup.
It was a third European title for world number 31 Cabrera-Bello, 33, and his first since 2012.
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Shinkwin, who beat Matthew Fitzpatrick to win the 2013 English Amateur Championship, played in last year's Open at Royal Troon but missed the cut.
Former US Open champion Graeme McDowell had hoped a first top-10 of the season would earn him a place at Royal Birkdale next week but he carded a 72 to finish on five under in a share of 19th.
The 37-year-old world number 102 has played in the Championship every year since making his debut in 2004.
France's Matthieu Pavon secured a major debut at Birkdale with a closing 66 to finish third, with Australia's Andrew Dodt claiming the last place ahead of England's Anthony Wall by virtue of his higher world ranking.
Dodt, the world number 193, had been scheduled to fly to New York on Monday for a holiday with his wife, but finished on eight under par alongside Wall, Padraig Harrington, Matt Kuchar and Ryan Fox.
Three-time major winner Harrington, who shared the lead after day two, fell away with a third-round 79 but closed with a 66.
Spaniard Rafa Cabrera-Bello birdied the first play-off hole to deny Callum Shinkwin and capture the Scottish Open.