The American was making his first visit to Leopard Creek but he was also making himself right at home as he opened up a six-shot lead at one point and led by four stood on the 16th tee.
That advantage was cut to one after a late wobble but Lipsky signed for a 68 and finished at 14 under, two shots ahead of Scotland's David Drysdale, with Scott Jamieson and Zander Lombard a further shot back.
Lipsky won the European Masters in 2014 in his first season as an Affiliate Member and had been a picture of consistency before securing just a single top ten last season.
That saw him finish outside the top 100 in the Race to Dubai Rankings presented by Rolex for the first time but he will not be fighting for his card in 2019 after handing himself the perfect Christmas present in Malelane.
“It’s indescribable actually,” he said. “Winning is what we all hope to do, it’s what we practise for, it’s what we all put the time in for - the blood, sweat and tears.
“This was a tough year for me. I haven’t played that well and have really struggled. To cap it off with a win at the end of the year is so special and I’m really looking forward to big things in 2019.”
Lipsky put his approach on the first to two feet to join the lead and took advantage of the par-five second, with a tee-shot to six feet on the par-three fifth edging him three ahead.
Home favourite Lombard had holed an 18-footer on the first and left himself a flick into the drivable sixth for a pair of birdies but bogeys on the seventh and eighth left him well back as he turned in 35.
Lipsky put an approach to five feet on the ninth to get to 14 under and while a holed bunker shot on the tenth kept Lombard in contention, Lipsky briefly led by six with another excellent approach to the tenth.
Lombard got within five with an approach to three feet at the 11th and Lipsky then made a first bogey of the day on the 12th.
A fantastic drive helped Lombard get on the green at the par-five 13th in two and he holed a 20-footer for an eagle, with Lipsky making a brilliant par after going in the water off the tee.
The lead was briefly down to one shot after Lombard holed from six feet on the 14th but Lipsky put his approach even closer and regained his cushion.
Lombard found water with his second on the 15th and saved par but put his tee-shot and third after a drop in the lake on the par-three 16th for a triple-bogey.
That meant the lead was up to four ahead of Drysdale who set the target with a 67.
The 43 year old holed a long putt on the fifth, made the most of the short sixth and then holed from the fringe on the ninth to turn in 32.
A bogey on the 11th set him back but he hit an approach to two feet on the 14th and got up and down for a birdie on the 15th.
A fortunate bounce out of the trees off the 18th tee then set up a closing birdie for him to get to 12 under and that was soon just one back after Lipsky got in trouble on the 16th.
He played away from the hole after finding a plugged lie in a bunker off the tee, missing the green and failing to get up and down to surrender a double.
An excellent two-putt on the 17th sent the leader up the last with a one-shot advantage and he got on the 18th in two for a closing birdie and a two-shot victory.
Lombard also birdied the last to move alongside 54-hole leader Jamieson who endured a roller coaster Sunday.
The Scotsman was four over for his round after ten holes with four bogeys and a double to go with two birdies but then made four gains in a row from the 13th before bogeying the 16th and picking a shot up on the last.
Oliver Wilson finished in the top ten for the first time in four years last week and he was there again after a 68 saw him finish at eight under alongside fellow Englishman Ben Evans, who also carded a 68.
Last week's winner Louis Oosthuizen was then at seven under alongside Swede Niklas Lemke, one ahead of Spaniards Adri Arnaus and Pablo Larrazábal, and South African Oliver Bekker.
Australian Deyen Lawson made the second hole-in-one of the season with an eight iron from 167 yards on the 16th to win a BMW 850 M.