Prince, who replaced regular captain Graham Smith earlier this week at the helm after Smith tore two ligaments in his left ankle, will also have to make do without specialist batsman and vice-captain Jacques Kallis.
To compound his woes, veteran bowler Shaun Pollock will also not take to the field because of paternity leave awaiting the birth of a child.
With Kallis recovering from surgery to fix a "tennis elbow", a niggling injury that has worsened in recent months, and Pollock not available, Prince will have a limited number of veterans to draw his inspiration from.
"I am inexperienced when it comes to the captaincy, but I am obviously delighted that I have been given the chance," he was quoted as saying in an interview with SuperSport.com.
With just 12 Tests under his belt, Prince said he would have to draw on the experience from other veteran players such as wicketkeeper Mark Boucher, Nicky Boje and out-of-form batsman Herschelle Gibbs.
"I'm sure the United Cricket Board could have looked at other candidates. Those candidates have a lot of experience and I will have the opportunity to draw from their experience," he said.
Left-hander Prince's breakthrough on the highest level came in 2000 and in his first Test against Australia that year he made a brave 49.
Following a second innings of 28 in the same Test, he has since gone on to make 1,089 runs in Test cricket and another 870 in One Day International.
His initial inclusion in the team prompted outcries of favouritism under the country's controversial quota system for black players, but Prince, who has long been highly rated by local cricket supremo Ali Bacher, showed his form with some valuable knocks in the middle order.
The last time South Africa toured Sri lanka, in 2004, they lost both the Test and one-day series.
Without Smith, Kallis and Pollock, South Africa are missing players with 251 Tests between them.
"Missing three premier players will have a huge effect on our team, but we have a good young side," Prince told www.cricinfo.com.
"We have a good pace attack with Makhaya Ntini, Dale Steyn and Andre Nel, and (spinner) Nicky Boje will play a role in conditions favourable for him.
"There is a nice balance in the attack and we must spread the load ... to get 20 wickets," he said.
He also had praise for the Sri Lankan team saying they were "playing very good cricket, having beaten England 5-0 in the one-dayers and drawing the Test series.
"On home ground they will be much more formidable, so its going to be a tough tour."
"The most important thing is to get the best out of the guys and to get them to perform in those conditions," said Prince.