The High Court also overturned the GMC's ruling last July that Sir Roy was guilty of serious professional misconduct. Mr Justice Collins said he had given "honest, albeit mistaken, evidence".
During Mrs Clark's trial in 1999, the paediatrician claimed the probability of two children in such a family dying naturally of sudden infant death syndrome was one in 73 million. The Royal Statistical Society later said the odds were nearer to 200 to one. Mrs Clark's conviction was quashed on appeal.
Professor Meadow, 73, retired from clinical practice in 1998, but wanted his reputation restored. He gave evidence in the trials of Angela Cannings and Donna Anthony, both of whom had convictions for murdering their children overturned on appeal. After the hearing, he said: "Children can be protected from abuse only if those who suspect abuse are able to give their honest opinion without fear of retribution. This is an important decision for paediatricians and all doctors, nurses, teachers and other professionals who may have to express difficult and sometimes unpopular opinions in the course of giving evidence in court."
Ruling on Professor Meadow's removal from the register, Mr Justice Collins said: "To erase someone such as Professor Roy Meadow, having regard to his record was quite unnecessary, particularly having regard to the fact that he has retired from clinical practice."
A spokesperson for the Royal College of Paediatrics and Child Health (RCPCH) said: " If the original decision had stood, there is a real danger that doctors across all specialities would have become reluctant to undertake vital expert witness work."
But the GMC is concerned that yesterday's ruling extends the immunity of expert witnesses from disciplinary action by their own regulator. The GMC stated: "Mr Justice Collins has extended the principle of immunity, so that it would apply for the first time to the bringing of disciplinary proceedings by regulators. The effect is to grant an immunity that, hitherto, has not been recognised in law."
Sally Clark's father said the outcome of the hearing was "academic". Frank Lockyer, a retired police superintendent, made the complaint which led to the GMC finding Professor Meadow guilty of serious professional misconduct. Yesterday, he said: "The GMC panel found he gave erroneous evidence and that doesn't change. The fact is the evidence was wrong. It's still wrong; it was wrong then and it's wrong now.
"A GMC panel of six, three of them doctors, considered what he did was serious professional misconduct. Today, a lone judge considers it wasn't. That probably says more about the system, that a judge can overturn six GMC people, three of them doctors."
Mrs Cannings said: "If an expert witness gives evidence in their field of expertise they should have no reluctance at all to go into a courtroom.
"It's when they are approached about areas outside their expertise then they should look up and say, 'Sorry, I can't deal with this', and actually step back.
The GMC had said Professor Meadows had "strayed outside his area of expertise" and abused his position as a doctor" by giving misleading evidence.