Kallis, unbeaten on 78 overnight, reached his 45th Test ton on day four of the second Test in Durban before he edged spinner Ravindra Jadeja behind.
The 38-year-old confirmed on Christmas Day that this Test would be his last and former England seamer Fraser told Sky Sports it is fitting for the all-rounder to bow out in style.
"It was a special moment for a special cricketer. He's a once-in-a-lifetime, maybe even a once-in-a-century cricketer and you've got to appreciate them while they're there.
"The fact that he's coped with all of the pressure and emotion about it being his last Test and has still managed to come through and produce a wonderful innings shows why he's a great.
"South Africa have got a big series against Australia coming up in the next couple of months and I'm sure they'd like to have him there for that.
"But if Jacques has made his mind up, I'm sure that's done. This is a perfect way to go out. Can he find a better way to go out than that?
"If he carries on and gets a couple of skittlers that knock his off pole out of the ground, then it won't feel the same."
Kallis' innings proved just enough to lift him up to third place on the list of all-time Test run scorers, a single run ahead of India's Rahul Dravid, with 13,289 from 166 matches.
The South African - who averages 55.37 with a highest score of 224 - is only 89 runs behind Ricky Ponting (13,378) but over 2,500 behind Indian legend Sachin Tendulkar.
However, Fraser said Kallis has to rival Sir Garfield Sobers as one of the greatest cricketers of all time because during his 18-year career he has also taken over 290 wickets and 200 catches.
"Statistically, he's the best ever all-rounder," said Fraser. "You'll have arguments with people about Sir Garry Sobers, who obviously was an unbelievable cricketer himself [scoring 8,032 runs at 57.78 and taking 235 wickets at 34.03 apiece].
"There is a romance that surrounds a cricketer of that generation and maybe he played with a more flamboyant, care-free style which people warm to.
"So in many people's eyes Sobers will always be the best but Kallis pushes him extremely hard and, arguably, is better.
"Of course, there have been a lot of other great all-rounders as well - Botham, Hadlee, Imran Khan - and they've produced wonderful statistics but sadly they don't come close to those of Kallis."
Watch highlights of day four of the second Test from 7pm on Sky Sports 2. Day five coverage begins at 7.25am on the same channel.