In a first round on January 28, conservative Anastasiades garnered 35.5 percent of the ballots, while communist-backed opponent Stavros Malas came second with 30 percent.
The head-to-head showdown is a rerun of the 2013 vote that saw Anastasiades cruise into office amid a financial meltdown in the Greek-majority European Union member.
But, with last week's losing candidates refusing to back either hopeful, this time around it looks set to be closer -- even though the former lawyer remains favourite to secure a second and final five-year term.
"In the future he will continue to do a lot on the economy and Cyprus problem."
Not everyone appeared so convinced by the incumbent.
"We need a change," said Nikolas Petros, 67, who had to close his business due to the economic troubles.
"In politics, especially the Cyprus issue, it has just been promises, promises. On the economy we have had too many problems."
As always, the nearly 44-year division of the eastern Mediterranean island between the internationally recognised Republic of Cyprus in the south and a Turkish-backed statelet in the north looms large.
Dovish former health minister Malas, 50, is one of the loudest proponents for finally reunifying the island and has slammed his opponent for not doing enough to reach an agreement.
The first-round success of the candidates seen as most keen on a deal has sparked hope that progress can be made.
But there remain major obstacles, including over the future of some 40,000 Turkish troops in the north, and deep scepticism that Nicosia or a nationalist government in Ankara are willing to compromise.
This time around the economy has been a dominant issue for the roughly 550,000-strong Greek Cypriot electorate as the island recovers from a 2013 financial crisis.
Anastasiades has claimed credit for an impressive recovery since agreeing a harsh 10-billion euro (more than USD 12-billion) bailout just weeks after taking power.
But major challenges remain despite record tourist numbers.
The economy is still smaller than before 2013, employment remains around 11 percent and banks are awash with bad loans.
Anastasiades has seized on this and warned ahead of the vote of a "return to the dogmatic policies that led us to the brink of bankruptcy".
After a lacklustre race, apathy appears high as no candidate has captured the imagination of voters -- especially young Greek Cypriots.
There was a record low turnout of just over 71 percent in the first round.
Polls close at 1600 GMT, with results and the inauguration of the next president expected Sunday evening.
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