The 38-year-old shot a five-under-par final round of 67, including a birdie-birdie finish, to claim one of the three Open spots on offer.
He was set for a three-man play-off for the title until Darren Fichardt birdied the final hole to win.
Manley's Open debut will come at Royal Birkdale from 20-23 July, 2017.
That will also be his debut at one of golf's four major championships.
Manley said: "I'm really chuffed to be playing in my first Major, I'm really excited.
"I've been trying for many years through pre-qualifying so to get there I'm pretty pleased.
"The Open is massive and I can't wait to get my teeth stuck into that golf course. I've never experienced anything as big as The Open before, but I can't wait for it."
Welsh golfer Stuart Manley has qualified for The Open Championship for the first time after finishing joint second at the Johannesburg Open.