In a unanimous judgment, five judges of the SCA bench ruled that the corruption and fraud charges against Zuma must stand - and gave Nicholson a tongue-lashing for his judgment, described as "incomprehensible".
"'Political meddling' was not an issue that had to be determined," said acting Deputy Judge President Louis Harms, while handing down judgment.
"Nevertheless, a substantial part of his judgment dealt with this question; and in the course of this discussion he changed the rules of the game, took his eyes off the ball and red-carded not only players but also spectators."
'Damage has been done'
However, the SCA ruled that it was too late to strike Nicholson's "political meddling" statements, as the "damage has been done".
"It makes no sense to strike them out at this late stage of the proceedings. The damage has been done. This does not mean that the order of the court below should stand," said Harms.
"Most of the allegations were not only irrelevant but they were gratuitous and based on suspicion and not on fact. The excuse for including them was unconvincing especially in the light of the disavowal of any intention to rely on them.
"The prejudice to the NDPP was manifest. Instead of having a short and simple case, the matter not only ballooned but burst in the faces of many. There may well be reason to hold that many of the allegations were vexatious and scandalous, but once again, it is not necessary to do so for present purposes."
The SCA was handing down judgment in an appeal brought by the National Director of Public Prosecutions (NDPP) against Nicholson's ruling in the Pietermaritzburg High Court on September 12.
Nicholson made two significant findings. The first was that the NDPP should have offered Zuma the opportunity to make representations before it decided to re-charge him in December 2007.
This finding by Nicholson effectively halted Zuma's prosecution but has now been overturned by the SCA, which means that Zuma is still facing charges of fraud, corruption, racketeering, and money laundering.
The second part of Nicholson's judgment was the finding that implicated political meddling in the decision to re-charge Zuma, a statement which ultimately led to the sacking of former president Thabo Mbeki.
Mbeki also applied to the SCA to have this struck out, but his application was dismissed.
'Judge's own conspiracy theory'
The judges of the SCA did, however, state that the findings made against Mbeki were out of order.
"The 'strategy' involving Dr [Penuell] Maduna [former justice minister], Mr Mbeki and all the other members of Cabinet as well as the casual connection between the [former chief prosecutor Bulelani] Ngcuka decision and Mr Mbeki and the Cabinet as found by the trial judge were not based on any evidence or allegation. They were instead part of the judge's own conspiracy theory and not one advanced by Mr Zuma," said Harms.
"It is important to stress that Mr Zuma did not allege that this decision was politically motivated; he did not say that it was unjustified; and he did not allege that Dr Maduna had acted improperly by being present at the press conference [when Ngcuka announced a prima facie case against Zuma].
"In spite of this, Judge Nicholson saw it as his duty to determine whether the decision was made from fear or favour."
Harms later added: "The court failed to have regard to another principle, namely that the more serious the allegation or its consequences, the stronger must be the evidence before a court will find the allegation established."
The SCA also criticised Nicholson's criticism of Mbeki's decision to dismiss Zuma as deputy president after his financial adviser Schabir Shaik was convicted on fraud in 2005.
"The propriety and legitimacy of Mr Mbeki's decisions were not issues in the case and he was never called upon to justify them. These matters are also not matters of law - they relate purely to political questions," said Harms.
Nicholson 'failed in his duties as a judge'
He said Nicholson failed in his duties as a judge in the September 2008 ruling.
"Judges as members of civil society are entitled to hold views about issues of the day and they may express their views provided they do not compromise their judicial office. But they are not entitled to inject their personal views into judgments or express their political preferences...
"Even if, in the words of the learned judge, the judiciary forms a 'secular priesthood' this does not mean that it is entitled to pontificate or be judgmental especially about those who have not been called upon to defend themselves," said Harms.
Also, several of Nicholson's findings were based on newspaper articles, which were "no more than inadmissible speculation by a journalist", said Harms.
"The trial judge... failed to comply with basic rules of procedure. Judgment by ambush is not permitted."
Guilt or innocence
Harms emphasised that the case before the SCA did not deal with Zuma's guilt or innocence, but dealt with legal technicalities.
Harms was referring to the NDPP's appeal against Nicholson's finding that the Constitution offers Zuma the right to make representations before being re-charged.
"[Zuma's lawyer] Mr Kemp J Kemp's reliance on the equal protection clause of the Bill of Rights is, accordingly, misplaced," said Harms.
"I therefore conclude that Section 179(5)(d) does not apply to a reconsideration by the NDPP of his own earlier decisions."
Harms also said that Ngcuka, the first chief prosecutor to raise the possibility of charging Zuma with corruption, made it "clear that if circumstances were to change in the sense that more or better evidence became available, the decision not to prosecute would be revisited and reconsidered.
"This means that the Ngcuka decision was not intended to be final; it depended on the then available evidence; and it was limited to the mirror images of the Shaik corruption counts," said Harms.