Al Nahda lost to eight-time champion Dhofar 2-3 in the return leg at the Al Saada Sports Complex in Salalah, but advanced to the final on the away goals rule following a 3-3 aggregate scoreline.
Guided by former Oman coach Hamad al Azzani, Al Nahda had defeated Dhofar 1-0 in the first leg at the Sohar Sports Complex on April 17.
Scoring two goals in Sunday's game proved to be decisive for Al Nahda, which is looking for its maiden HM's Cup title.
It will face 2009 winner Suwaiq, which sealed its place in the final on Saturday despite a 0-1 defeat to Al Arouba at the Sur Sports Complex.
Suwaiq advanced with a 3-1 aggregate score, having won the first leg 3-0 at the Seeb Sports Stadium on April 16.
On Saturday, three-time winner and hosts Arouba took an early lead through Hameed in the 26th minute to raise hopes of a fightback.
But the Suwaiq defence stood firm to ward off a series of attacks and eventually book its berth in the final.
The final will be played at the Sultan Qaboos Sports Complex on May 26.
H E Ali bin Masoud al Sunaidy, the Minister of Commerce and Industry, will preside over the title showdown as the chief guest and give away the prizes.