Ahli-Sidab dominated the first half an hour of the contest, winning the session 12-9.
But a dogged Muscat players rallied to win the second period 14-10, eventually securing a narrow 23-22 victory.
Muscat's experienced forward and national team player Assad al Hassani provided his team a crucial one-point lead just five minutes before the final whistle.
Also, Muscat's shot-stopper Hussain al Jabri pulled off a few sharp saves in the dying minutes of the game.
Muraad Busabti, Muscat's Tunisian coach, said, “It was a difficult match and I knew it would be close.
“Both the teams have faced each other before in the league this season, winning one game each. So, the final was going to be close.”
Ahli-Sidab’s coach Khalil al Mashari said, “It was a good contest. Both the teams deserved to be in the final after a really tight season. It is disappointing to lose by just one point, but we fought hard till the end.”
Seeb finished third in the eight-team league.
H E Abdulmunim al Hasani, Minister of Information and Broadcasting, was the chief guest at the final and gave away the prizes along with Sultan al Hosni, chairman of the Oman Handball Association (OHA).
Individual awards: Best player: Hamad al Dugaishi (Ahli-Sidab), best playmaker: Imad al Dugaishi (Ahli-Sidab), best leftback: Taha al Raisi (Seeb), best rightback: Ahmed al Hinai (Seeb), best left-winger: Nasser al Tamtami (Muscat Club), best right-winger: Assad al Hassani (Muscat Club).