The Yorkshire title holder came from two shots back going into the last day to lift the prestigious Brabazon Trophy with rounds of 67 69 70 70 at the London Golf Club.
His county team-mate Ben Hutchinson, of Howley Hall, placed sixth (71 68 71 71) and Dan Brown (Masham) earned 18th place with rounds of 71 69 77 71 alongside Lindrick's Bailey Gill (70 74 74 70).
Bower, twice a winner in South Africa earlier this year while on tour with England Golf men's squad, pulled level with Australian Cameron Davis, the 54-hole leader, as early as the second hole.
He birdied as Davis bogeyed and when Bower also birdied the fourth for the third time in four rounds he moved one ahead.
However, the fifth hole saw a three-shot swing in favour of the Australian when he birdied and Bower stumbled to a double bogey seven.
The Yorkshireman showed great poise by birdieing eight to be just a shot adrift and when Davis bogeyed 10 the pair were level again.
Bower birdied 11, but his lead was short-lived as David responded with a birdie of his own at the next.
Both men dropped a shot at the 14th and birdied the 15th before Bower shed another shot at 16 to trail with only two holes remaining.
His response was emphatic and a birdie at 17 drew him level before drama at the final hole.
With Bower and Davis locked at 12 under par, a violent thunderstorm forced the last group off the 18th green as they prepared to putt and when they returned Bower two-putted for par and victory, while Australia’s Davis missed a short one that would have taken the battle into a play-off.
Bower's victories in the Gauteng North Open and Southern Cape Open helped lift him from outside the world's top 100 amateurs to 38th place and his triumph in the Brabazon Trophy should see him into an even loftier position.
He was watched in London by his grandparents, Tony and Jean, and his girlfriend Olivia Stephenson and afterwards described it as "the biggest win of my life by an absolute mile".
He added: "It means everything, I can’t express it, I’m just delighted.
“But I feel really bad for Cameron, he played really well and it was awful for that to happen on the 18th. No one wants to see that and you would rather win it by holing a putt.”
For the last couple of months Bower has felt his performances have been “very average”, but he has worked successfully with his swing coach, Alan Thompson, of Heswall.
“He has been absolutely instrumental,” said Bower.
It also continues a superb run by England internationals, following Alfie Plant’s win in the Lytham Trophy and Scott Gregory’s victory in the Amateur Championship. The next challenge is the European Team Championship in France in early July and Bower said: “We’ve got a great team and I really want to do my best for the country in that.”