A closing round of 78, including that penalty, saw the Moor Park, Hertfordshire, player finish on 293, five over par, for a single stroke victory over Erik Myllymaki of Finland at Bogota.
"This win was unexpected,” he said. “I never thought that I’d do well this week because I couldn’t get to grips with the course on the first day and only found the pace on the second,” added Shinkwin, after he and Jordan Smith had been delayed in arriving in the country at the beginning of the week.
After an opening 75, which left him three strokes off the pace, Shinkwin produced his best golf over the next 36 holes. A second round two-under-par 70 saw him two shots clear of the field, which he reproduced in round three to go into the final round with a healthy six-stroke lead.
He was clearly the man to beat but he found the closing day far from easy. His final round 78, his worst of the week, contained only one birdie, five bogeys and a double bogey.
Most of the dropped shots came from the tenth to 13th holes and culminated in the penalty incurred on 13 when he breached the rules of the competition by practising a putt. But a par on the 14th plus the lone birdie on 17 got him back on track and he held on to take the title.
"For me it is a very exciting victory”, he said. “I lost my grandfather recently while this is my first tournament of the year after five months without playing.
"Consistency was the key. On the first day I hit 14 fairways and finished three over. I made only six in round two and finished two under. It was a constant struggle but exciting," said Shinkwin, who has his sights set on Walker Cup selection this year.
The Finn, Myllymäki, finished with a third consecutive 73 for the runners- up spot on 294, two better than Peruvian Joaquin Lolas, who returned one of the two best scores of the final day of 71.
Smith, who was on the leaderboard for most of the week, finished equal seventh on 301 after a closing 79.
Leading final scores: Men: 293 C Shinkwin (Eng) 75 70 70 78; 294 E Myllymaki (Fin) 75 73 73 73; 296 J Lolas (Peru) 77 72 76 71; 298 A Tosti (Arg)
80 74 73 71; 299 J Shufflebotham (Wal) 77 77 70 75. Other England score: 301 J Smith 75 75 72 79. Women: 299 B Henderson (Can) 73 75 76 75; 305 D Darquea (Ecu) 75 76 78 76, J Keel (Can) 78 76 76 75. England scores: 318 A Peters 83 75 81 79; 322 S-J Boyd 79 76 85 82
Image Callum Shinkwin copyright Tom Ward Sport Photography