The South African cleric said that Mr MacAskill’s decision to free Abdelbaset Ali Mohmed al Megrahi, who has terminal prostate cancer, should be "commended".
The move sparked controversy, as some families of the 270 victims of the bombing criticised the decision and President Barack Obama told Gordon Brown of his "disappointment" that Megrahi had been released.
But in a message sent to the Scottish Government, Archbishop Tutu welcomed Megrahi’s release from Greenock Prison. "I believe the Scottish Justice Secretary’s decision to release Mr Megrahi on compassionate grounds is to be commended," said the former Nobel Peace Prize winner.
"One understands the anguish of family members and friends of the victims but they honour their memory more by being compassionate than retributive."
The 77-year-old added: "The outcry has been caused not so much by the release as by the welcome he got in Libya. These two issues should be separated."
His message was sent as the health of Megrahi, the only man to be convicted over the bombing of Pan Am flight 103 over Lockerbie in 1988, is reported to have deteriorated markedly.
His lawyer, Tony Kelly, said he could not "confirm or deny" the claims, but Megrahi’s brother, Abdenasser, said: "He is at a special ward at Tripoli Medical Centre. His condition has deteriorated rapidly. He is unable to speak to anyone."
Archbishop Tutu is the second world figure to back the release, after Nelson Mandela also welcomed the move.
SNP Westminster leader and foreign affairs spokesperson, Angus Robertson, said: "The fact is that many people from across the parties, the legal fraternity, churches, civic Scotland and throughout the world have endorsed Kenny MacAskill’s difficult decision to send Megrahi back to Libya to die.
"Archbishop Tutu’s views demonstrate that there is a great deal of international respect and support for what was a compassionate decision by the Justice Secretary."
Campaigners are pressing ahead with calls for the UN General Assembly to hold an inquiry into the bombing after Megrahi dropped the second appeal against his conviction just before his release.
Asked about the chances of success, Professor Robert Black, one of the original architects of the trial at Camp Zeist, said: "I think it’s pretty good. There are a lot of countries that don’t think we’ve seen the truth and would like to see that uncovered."
Meanwhile, there was confusion over whether any trial in the case of a policewoman murdered outside the Libyan embassy in London 25 years ago would take place in Britain.
A newspaper reported that an agreement was secretly struck three years ago, when trade deals worth hundreds of millions of pounds were being negotiated with Tripoli, that would result in Yvonne Fletcher’s killer going on trial in Libya.
Ms Fletcher’s mother said she had not been informed of a deal and Tory MP Daniel Kawczynski, chairman of the all-party parliamentary group on Libya, accused the Foreign Office of "deliberately misleading" the family.
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