'Miscarriage of justice'
Judges had thrown out charges against Haradinaj for lack of evidence, during a trial marked by the reluctance and witnesses to testify.
"The trial chamber failed to take sufficient steps to counter witness intimidation that permeated the trial," Robinson said.
"Given the potential importance of these witnesses to the prosecution's case, the error undermined the fairness of the proceedings and resulted in a miscarriage of justice."
Haradinaj, 42, and Idriz Balaj, 38, who allegedly headed a paramilitary unit, were acquitted in April 2008 on numerous counts of war crimes and crimes against humanity.
Co-accused Lahi Brahimaj, 40, a deputy commander of the KLA and ran the Jablanica prison camp, was convicted of torture.
Haradinaj, the most senior Kosovo leader to stand trial at the ICTY, was a commander of the KLA at the time of the alleged atrocities, as was Balaj.
He showed no emotion as Robinson ordered the retrial and told guards to take the former leader into custody.
No date has been set for the trial.
Michel Abdel Massih, an international lawyer based in London, told Al Jazeera that it was "highly unusual to reverse an acquittal".
"What is interesting in this case is that the judgement of the court of appeal was not unanimous, it was by majority and there was a strong dissenting opinion by judge Robinson, who is a very experience international lawyer.
"The fact he gave a dissenting opinion, to me, tends to suggest that there are matters here that need to be looked at very, very closely."
The development comes a day before the International Court of Justice rules on Kosovo's independence from Serbia.
Serbia lost control over Kosovo in 1999 when Nato bombed it to halt the killing of ethnic Albanians in a two-year counterinsurgency war.
After nine years under an international mandate, the Albanian majority, backed by the United States and most EU member states, declared independence, which Belgrade vowed never to accept.
Serbia hopes the ICJ decision, which is only advisory, can help restore its claim on the Balkans' smallest country, one of the poorest corners of Europe.