The R&A ranked world number one player fired a three-under par 70 in the final round to become the first Englishman to win the title and clinch the number one seed for the match play starting on Friday.
But there was no place in the draw for Irish duo Shane Lowry and Paul Cutler.
Irish No 1 Lowry finished one shot outside the top 32 qualifiers on seven-over par after a closing 75 with Cutler on 11 over after a 77.
Beginning the day four shots behind Younger, Willett started with birdies on the first and third holes to start building momentum.
Back-to-back bogeys on seven and eight halted the English charge but he steadied his nerves to play the back nine in two-under despite the challengers nipping at his heels.
Younger's title chase got off to a disappointing start as the Victorian recorded just two pars in his opening eight holes among a string of bogeys. The AIS/Golf Australia National Squad member made amends on the back nine with a three-under, but it wasn't quite enough to atone for his early misses.
Grant Scott was six strokes back after round three but put together a final round charge to send a scare through the world number one. Scott birdied all four of the back nine par fours to post an equal tournament-best round of 69 but in the end, the New South Welshman had to settle for equal second place.
The focus remains on Royal Adelaide for the match play component of the Srixon Australian Amateur Championships beginning on Friday morning. The top 32 men and women qualifiers from the stroke play will battle it out in sudden death until just two are left at the conclusion of play on Sunday.
Defending men's champion Rohan Blizard qualified safely after a final round 72 and former champion Tim Stewart will also be looking to repeat after overcoming early hiccups to also post a one-under 72 and punch his match play ticket.