His rival Stavros Malas from the left-wing Progressive Party of Working People (AKEL) was backed by 44.01 percent of the voters, the ministry said.
Anastasiades, who ran in the election as a candidate from the center-right Democratic Rally (DISY) party, thus secured a second five-year term as president of Cyprus.
The turnout at the vote was 73.97 percent.
The name of the president-elect will be officially announced during a special ceremony at 10 p.m. (20:00 GMT). The swearing-in ceremony is scheduled for February 28.