Pakistani selectors said Akhtar lacked fitness for a five-day Test despite bowling 21 overs in a four-day first class match and featuring in a domestic Twenty20 tournament.
"There must have been some compelling reasons to keep a bowler like Akhtar out of the team, reasons we don't know," Imran Khan told AFP.
The Pakistan team will leave on Tuesday and open the tour with a three-day game against South Africa A' at Kimberley from January 6, before playing the first Test at Centurion from January 11.
Khan, who played 82 Tests for Pakistan and was among the world's top four allrounders in the 1970s and 1980s, said it was tough to keep a match-winner like Akhtar out.
"It is tough to keep a fully fit Akhtar out of the team - he is a match winner. If selectors feel he is not fit, then they must watch him in a match, and if found fit he should be sent on the first available flight," said Khan.
Sarfraz blames Inzy for Shoaib's ommision: Khan's former new-ball partner, Sarfraz Nawaz, lambasted the selectors for omitting the pace duo of Shoaib Akhtar and Shabbir Ahmed for the tour of South Africa and claimed the fitness reason was a eyewash and it was a spat with captain Inzamam-ul Haq which cost the "Rawalpindi Express" his place in the side.
In an interview with Pakistan Press International (PPI), the former fast bowler rued personal ego had been put ahead of national interest in this case.
"I have been informed by my sources that Inzamam and Shoaib exchanged hot words during the training camp held at the Gaddafi Stadium while a few other members of the team were also against the inclusion of Shoaib Akhtar."
"I do not know why we always put our personal interests over our national interest," he said.
"Now with Akhtar not in the team, South Africa will prepare fast pitches, as there would be little pressure on them," said Nawaz, who played 55 Tests for Pakistan.
Former medium-pacer Aaqib Javed said questioning of Akhtar's fitness was surprising to him.
"I watched Akhtar bowl in the Twenty20 and I saw no reason to question his fitness, but I think selectors have different ways," said Javed, who played 21 Tests for Pakistan.
"But having said this, I expected Akhtar to be 100 percent fit after he missed cricket due to the doping issue.
"I think the selectors should have still sent him and waited for the second and third Test, because you need to have match winners in the squad, as it keeps pressure on the opponents."
The 31-year-old Akhtar has not played for Pakistan since a one-day match against England three months ago. He was banned for two years, and fellow paceman Mohammad Asif for one year, last month after both tested positive for the banned steroid nandrolone in October.
However, a Pakistan Cricket Board appellate committee overturned the bans earlier this month on the grounds that both did not take the banned substances knowingly.
The World Anti-Doping Agency (WADA) has challenged the decision and the Court of Arbitration for Sport (CAS) is likely to hear WADA's appeal this week.