After both the teams failed to find a breakthrough in regulation-time, the match went directly to the tie-breaker.
Sadiq Adam, Salles de Silva and Hussain al Ghilani scored for Saham, while Seeb's two goals were netted by Amar Rahman and Said al Farsi.
The first half of the final was played on Thursday. Heavy rain intervened during the break and washed out chances of play later that evening and match officials were forced to reschedule the rest of the title clash for Saturday.
Last month, Seeb had made it to the final after coming from a goal down to defeat Al Nasr Club 2-1 in the first semifinal at the Sultan Qaboos Sports Complex (SQSC).
Later, on the same day, Saham had shocked strong contender and eight-time domestic league champion Fanja Club 1-0 in the second semifinal.
Sayyid Khalid al Busaidi, the Oman Football Association's (OFA) chairman, gave away the trophy and medals to the winning team at the prize distribution ceremony.