Neil added a 72 to his earlier rounds of 70, 66 and 67 to finish 13 under par on 275 and was edged out by Jason Smith, of the host nation, who made up three strokes on the Scot to win with a 14-under-par total of 274, after a final-round 69 to add to earlier scores of 71, 66 and 68.
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The Scot cancelled out two bogeys before dropping another shot to par at the 17th and was left needing an eagle three at the last to tie with Smith; he could only secure a birdie. The South African covered the last seven holes in three under par.
Finishing alongside Neil was Irishman Dermot McElroy, the halfway leader, who had rounds of 69, 65, 70 and 71 for 275. He too birdied the 18th to gain a share of second place.
Neil said: "I'm pretty disappointed, because I played my poorest round on the final day. I feel I let myself down, but all credit to Jason. Out there you are trying your hardest to win and Jason held up best under pressure."
Ewen Ferguson, the British Boys' champion from Bearsden, tied for 19th place on 281 with a 72. Scott Gibson (Southerness) shot 70 for 282 and Cawder's Jamie Savage was joint 24th on 283 after a 71. Left-hander Bob McIntyre (Glencruitten) finished on 284 after a closing 72 to finish 27th.
The Scottish competitors continued a fine national tradition at the tournament, with Fife's Brian Soutar winning in 2012 and Aberdeen's David Law coming runner-up in 2011.