The defending champions lifted not only the gross trophy in the 54-hole stroke play event, but were also net winners.
The competition attracted more than 100 players from across the country to Southport and Ainsdale where the team competition saw the best four scores from six count.
In tough conditions, Balby's captain Nathan Fell, a one-handicapper from Lindrick, hit a six-over-par 78 in the first round and a par 72 in the afternoon on day one.
His Lindrick club-mate Greg Denton (scratch) carded, 80 77, Rotherham's Aaron Nairn (one) 73 81, and Hickleton's Luke Palmowski (one) 72 73.
Six-handicapper Tom Guttridge, of Sandhill/Rotherham, made his college debut and shot two rounds of 82, while Garforth's Laura Morrison (three) carded 83 79 against the ladies’ par of 75.
It left Morrison third overnight in the girls' gross competition while Balby took a 14-shot team lead into the final round.
On day two, in perfect conditions, Guttridge, Denton and Fell shot 76, Palmowski 79, and Morrison and Nairn 80.
Their efforts enabled Balby to win by four shots from Myerscough College and take the net honours.
Palmowski missed out on a play-off for the individual title by three shots and Fell by five.
Balby's Golf Academy director Ian Lindley said: “It was a special week at a prestigious golf course on the west coast and they have a chance to win it for a third time next year.
“It was sweet revenge as Balby had lost by a single shot to Myerscough College at the AOC Sport Golf finals at St Andrews in March.
“This now leaves us with an impressive tally of two national titles and a runners-up position.”
The squad will head to Trevose, Cornwall, for the British Schools and Colleges finals, and also to Woodhall Spa, Lincolnshire, for the English Schools Team Championship, where they will represent Yorkshire schools.