A bench of Justices S Muralidhar and Vinod Goel reversed a trial court's verdict which had acquitted the accused.
The high court convicted the 16 former Provincial Armed Constabulary (PAC) personnel for murder, kidnapping, criminal conspiracy and destruction of evidence under the Indian Penal Code.
It termed the massacre "targeted killing" of unarmed and defenceless persons by the police.
All the 16 convicts have retired from service.
The high court's verdict came on pleas challenging a trial court's decision to acquit 16 policemen of charges of murder and other crimes in the case.
The high court had on September 6 reserved its verdict on the appeals filed by Uttar Pradesh, the National Human Rights Commission (NHRC) and some private parties including a survivor of the massacre, Zulfiqar Nasir.
It had also reserved its judgement on BJP leader Subramanian Swamy's plea seeking further probe to ascertain the alleged role of the then Minister of State for Home P Chidambaram in the case.
The court had on February 17, 2016, tagged Swamy's plea with the other petitions in the matter.
On March 21, 2015, a trial court here had acquitted the 16 former PAC personnel giving them benefit of doubt, saying their identification could not be established due to lack of evidence.
Nineteen people were named as accused and charges were framed against 17 of them for offences of murder, attempt to murder, tampering with evidence and conspiracy, by the court here in 2006.
The case was transferred to Delhi on a Supreme Court direction in September 2002 following a petition by the families of the massacre victims and survivors.
Of the 17 accused, 16 were acquitted while one died during the trial.
The NHRC has intervened in the matter seeking further probe into the massacre in the Hashimpura locality of Meerut in Uttar Pradesh.
A trial court had on March 8, 2013, dismissed Swamy's plea for the further probe to ascertain the role of Chidambaram, who was a Union Minister between 1986 and 1989, in the incident, saying he has no locus standi and it is only the police who can move an application for further probe.
Thereafter, Swamy had approached the high court with the appeal.
(With inputs from agencies.)