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Tonight thousands of his supporters have gathered in Metaxas Square, Nicosia, to celebrate his historic victory, honking horns and letting off fireworks.
The final result only became clear at 2000 hours local time. The archbishop won 144,501 votes, while his rival John Clerides took 71,753.
One of the first people to hail the archbishop's success was the leader of the Turkish community, Dr Fazil Kutchuk, once one of his bitterest rivals but now a staunch ally and soon-to-be vice-president.
Dr Kutchuk expressed his delight that "the man who has acted as leader of the Greek community for so many years should have achieved the success which, beyond doubt, he deserves".
He went on to say he was confident the two men could work together to ensure the new Cyprus Government was established on time.
The polling authorities say the system of supervising and scrutinising the elections has been exceptionally thorough. Every conceivable step has been taken to ensure complete accuracy and impartiality.
In his first public statement since being declared president, Archbishop Makarios has called on Greeks and Turks to co-operate "in a spirit of sincerity, absolute respect for each other's rights and real understanding of communal interests and deserts".
It has been a remarkable turnaround for the Archbishop, who three-and-a-half years ago was deported to the Seychelles by the British authorities for his refusal to renounce the violent campaign by EOKA terrorists to rid the island of its colonial rulers.
He returned to Cyprus in March to a tumultuous welcome after agreeing to give up his campaign for enosis, or union with Greece, in return for Cyprus's independence.
Talks in London in February finally saw a deal signed between Greece, Turkey and Britain which formally brought to an end EOKA's terrorist campaign and four years of fighting in which hundreds had died.
Colonel Grivas, leader of EOKA, has publicly announced he is giving up the leadership and leaving Cyprus.
Under the terms of the deal, a Greek Cypriot will be president and a Turkish Cypriot will become vice president. All claim to enosis has been abandoned. As part of the deal, Britain is allowed to retain two military bases on Cyprus.
Archbishop Makarios and Dr Kutchuk formally negotiated Cyprus's independence from Britain, which was officially declared at midnight on 15 August 1960.
Cyprus became a member of the Commonwealth in 1961.
Conflict between the Greek and Turkish communities has continued to be a problem.
In 1974, Makarios was briefly deposed in a coup by Greek Cypriots seeking unification with Greece. Fearing for the rights of the minority Turkish population, Turkey invaded northern Cyprus and expelled the Greeks from the north.
The island was officially divided and the buffer zone between the two sectors is still patrolled by the United Nations.
On his death in 1977 the posts of archbishop and head of state were officially separated.
In 1983 Turkey named the northern sector Turkish Republic of Northern Cyprus. This is not recognised by the international community, which only recognises the southern two-thirds of the island, the Republic of Cyprus.
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