Jones had a three-shot lead heading into the final round at the Australian GC but a two-over 73 almost saw his second PGA Tour title slip away.
The Australian was three over for his round after two holes, a bogey on the first immediately followed by a double at the first par three.
Jones recovered with two birdies but a triple-bogey seven on the ninth left him with work to do on the back nine. But he picked up two shots on his way in to claim victory by one stroke from major winners Scott and Spieth.
Jones said : “I got the job done. There was a lot of stress and a lot of anxious moments but I came through with that lipping put on the last to get the trophy. “To have my name on the this trophy with (Jack) Nicklaus, (Jack) Newton, (Greg) Norman, all those guys, is a dream come true for me and something that can never be taken away.”
Scott started the day nine shots off the pace but ended just one stroke behind after picking up seven birdies in his six-under 65.
Spieth bogeyed three of the first six holes but fought back to finish evens for the day to join Scott in second.
The 2014 Masters and US Open champion also saw his course record surpassed.
Australian veteran Rod Pampling went two better than the mark Spieth set last year with a 10-under 61 to finish two shots off the pace.
Meanwhile home favourite Charl Schwartzel claimed a fourth career success at the Leopard Creek course in Malelane to win the Alfred Dunhill Championship.
The South African took a three-shot lead into the final round and never looked like losing despite dropping two shots in his first nine holes as he finished 15 under par.
Schwartzel finished four shots ahead of Gregory Bourdy in second and five clear of third-placed Benjamin Hebert after a two-under-par fourth round.
Bourdy hit four consecutive birdies before a triple-bogey on the par three seventh hit his challenge, despite a mini-recovery late on when he claimed birdies on the 15th and 16th. Hebert dropped a shot on the 18th to hand Bourdy outright second.
Schwartzel eased to victory, mainly thanks to a 66 and 67 in his first two rounds. Bogeys at three and eight briefly stalled Schwartzel’s charge but birdies at 11, 13 and 14 ensured he maintained a comfortable lead.