The wet and windy conditions meant the event was restricted to 54 holes rather than its usual 72-hole format.
Gill had taken a 10-shot advantage into the final day's play after successive rounds of 65 for a six-under-par 36-hole aggregate.
The Welsh Open Youths’ champion added a 78 on Wednesday for a final total of 208.
His club-mate Nathan Fell finished eighth (75 71 79), Huddersfield's Josh Morton placedjust outside the top 20 (75 73 85) while Howley Hall's Tom North climbed into the top 30 by adding a final round of 79 to his opening rounds of 77 82.
Fulford's Charlie Thornton began with rounds of 74 78, but had a No Return on Wednesday.
Past winners of the event include European Tour player Tyrell Hatton, the current world No 14, who took the title in 2011.
The silver salver was presented to Bernard Darwin by The Times newspaper and is open to players under the age of 21 on January 1 in the year of competition.
Only 50 players are selected from those with the lowest handicaps, the number having special relevance as it commemorates the fact that Darwin was twice captain of Rye, in 1906 and 1956, a gap of 50 years.