"We are excited and happy," Sertoglu said by telephone from FIFA headquarters in Zurich. "It can help politicians to make progress as well."
Cyprus's head of state, President Nicos Anastasiades, expressed his "deep satisfaction" with the agreement which must be ratified at the assemblies of both football bodies.
The Cyprus FA president, Costakis Koutsokoumnis, called it a "historic" day for the nation's football, though his organization cautioned against drawing political meaning.
"The arrangement concerns only football matters and doesn't constitute a precedent for the political problem of Cyprus, and it is also temporary until a Cyprus settlement can be achieved," the CFA said in a statement.
FIFA president Sepp Blatter, who attended the meeting with UEFA President Michel Platini, praised the parties for their "outstanding contribution to this milestone arrangement."
"Both the Cyprus Football Association and the Cyprus Turkish Football Association are today providing the whole world with an excellent example of how football can build bridges and bring people together after a long period of conflict," Blatter said in a statement.
The island's two football bodies split in 1954 following a Greek-Cypriot uprising against British colonial rule. Cyprus was divided in 1974 when Turkey invaded the north after a coup by supporters of union with Greece.
"Obviously, this is the first step. We have some problems which must be resolved," Sertoglu said. "We will not have a separate national team but we hope in the future we will be a unified league."
Based in the divided capital city Nicosia, Cetinkaya would have ambitions to become the first Turkish-Cypriot club to play in UEFA's club competitions.
Cetinkaya won its 14th league title last season, and also won league and cup trophies in the united Cyprus in the early 1950s.
"For the young generation it will have a really high motivation, and it will give them the chance to play in the international arena," Sertoglu said. "We will continue with our own leagues but some of our clubs ... will join with a unified league. But the number of clubs and time of this is not certain. This is why we are not 100 percent satisfied."
A steering group including CFA and CTFA officials will work on the details of the provisional agreement.
"The arrangement, which is based on the FIFA and UEFA statutes and only concerns football-related matters, aims to unify and facilitate the progress of football within the football communities on the island of Cyprus through a relationship based on trust, mutual respect and goodwill," FIFA said.
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Associated Press writer Menelaos Hadjicostis in Nicosia, Cyprus, contributed to this report.