Both main parties saw their support drop, but Mr Papadopoulos's centrist DIKO - which led Greek Cypriot opposition to the UN plan in a referendum two years ago - increased its share of the vote to 17.9 percent, according to final results.
Its main coalition partner AKEL won 31.2 percent, just ahead of the right-wing opposition DISY party on 30.3 percent, both down on the last election but maintaining their traditional dominance.
The coalition, which also includes socialist EDEK that won 8.9 percent of the vote, is expected by observers to hold together in the next parliament despite the parties' disparate political positions.
Chief Returning Officer Lazaros Savvides confirmed AKEL and DISY receive 18 seats apiece in the new 56-member parliament and DIKO 11.
EDEK clinched five seats, DISY splinter the European Party won three and the Greens managed to retain their lone seat.
"The government, strengthened by the overall messages of these elections, continues its work in order to fully implement its programme," Mr Papadopoulos told reporters after polling stations closed.
AKEL Chief Demetris Christofias said the election results belied pundits' predictions of a massive loss for the party following a deeply divisive internal debate over the UN reunification plan that had threatened to tear it in two.
DIKO deputy leader Nicos Cleanthous saw the election results as a "reward" for Mr Papadopoulos's and the party's "conscientious and unwavering" stance on the Cyprus problem.
About 500,000 voters were registered for the election, which saw a record 487 candidates in the running, including a Turkish Cypriot for the first time in more than four decades.
Some 270 of the island's minority Turkish Cypriots were also allowed to vote for the first time since 1963, when Greek Cypriot leaders unilaterally sought to amend the power-sharing constitution adopted when Cyprus became independent from Britain in 1960.
To register, Turkish Cypriot voters had to prove their main residence is in the southern two-thirds of the island controlled by the internationally recognised Cypriot government, and not in the breakaway state which Turkish Cypriot leaders declared in 1983.
Turkish Cypriot poet Neshe Yashin was on the ticket for the United Democrats, a small left-wing faction which strongly supported the UN plan.
But the party fell short of the 1.8 percent threshold to retain its sole seat in parliament.
"We acknowledge that Cypriot society doesn't accept our message, but at the same time, we feel completely at ease with our conscience for having fought an honourable and patriotic fight for the good of this place," United Democrats chief Michalis Papapetrou told reporters.
Greek Cypriots overwhelmingly voted down the UN reunification blueprint in a referendum just over two years ago, although it was backed by the rival Turkish Cypriot community.
Sunday's election was the first in the government-controlled south of the island since the plebiscite and since a divided Cyprus joined the European Union in May 2004.
The results suggest that Mr Papadopoulos will head into a presidential election in two years' time confident of clinching a second five-year term and a renewed mandate for his tough approach on future efforts to reunify the island.
Mr Papadopoulos has insisted he is ready for new reunification talks after the election, and both Washington and UN chief Kofi Annan have registered their support for a fresh peace push.
EU Enlargement Commissioner Olli Rehn on Friday urged the international community to use a "certain window of opportunity" provided by the election to help relaunch peace talks.
But asked by a Turkish Cypriot journalist whether the elections would prompt significant changes in his government's position, Mr Papadopoulos said: "I don't see any reason for any dramatic change."
Voting in Cyprus is compulsory, but there have been no prosecutions in years.