"The choice is between this settlement and no settlement," he said on Wednesday after marathon talks with leaders of Cyprus's Greek and Turkish communities as well as the Greek and Turkish prime ministers to settle the 30-year crisis.
The talks were aimed at reaching a deal on a revised blueprint drawn up by Annan aimed at reunifying the Mediterranean island before it is due to join the European Union on 1 May.
"If the referendum is approved, Cyprus will be reunified in time to accede to the EU," the UN secretary-general said.
Annan had given the delegations until midnight on Wednesday to support his proposals, or to see them put to a vote across the divided island without their backing.
But the island's rival communities failed to reach an agreement between themselves in the week-long negotiations at a secluded hotel complex in the snow-covered Swiss Alpine resort of Buergenstock.
"Unfortunately it proved impossible to reach an agreed solution," Greek Prime Minister Costas Karamanlis said late on Wednesday. "It is now up to the people of Cyprus and its political leadership to make a final decision."
Annan appealed to the two communities to vote "yes" in the referendum to be held on 24 April.
"There have been too many missed opportunities in the past. For the sake of all of you and your people, I urge you not to make the same mistake again," Annan warned.
"For the sake of all of you and your people, I urge you not to make the same mistake again"
But Annan said his plan, which establishes a loose federation with Greek and Turkish Cypriot areas and a central government, "offers the best chance for peace, prosperity and stability that is ever likely to be on offer."
"We have tried to accommodate the express concerns of both sides to create a win-win situation," he said. "I believe we have succeeded."
Turkish Cypriot reaction
Turkish Cypriot leader Rauf Denktash on Thursday rejected the final version of the UN plan he said was not satisfactory despite a number of favourable changes.
"There are amendments in our favour, I do not want to be unfair, but in its current form, I do not see anything to vote 'yes' to," the veteran leader said.
The division of Cyprus has taken on greater urgency with the looming expansion of the European Union on 1 May, when the island, along with nine other countries, is due to become a member.
But if either side rejects the proposals in the referendum, only the internationally recognised Greek south will enter the European Union, leaving the Turkish Cypriots out in the cold.
A failure to help broker a deal on Cyprus could also hamper Turkey's own EU ambitions. The mainly Muslim country hopes to obtain in December a date to start EU accession negotiations.