The win helped Rasheed Jaber's boys hopes of qualifying alive for the AFC U19 finals in Indonesia next year after it finished runner-up in the group, surviving a scare from Bahrain.
In a late game on Wednesday, Bahrain upset leader UAE 1-0 to come level with Oman with seven points each. But Oman's better goal-difference tilted the scales in its favour as it ended second behind UAE, which qualified directly for the finals.
Oman, which was held by Bahrain in their previous encounter, needed a win against Nepal to keep its hopes of advancing into the next round as one the best five runner-up teams.
Oman opened its account in the 11th minute through captain Faisal al Harthi via a brilliantly executed free-kick which gave Nepal goalkeeper Sojit no chance.
Oman doubled its advantage when Arshad Said al Alawi scored after a one-on-one opportunity with Sojit in the 32nd minute. Harthi completed his double in first half added-on time, to put Oman 3-0 up at half-time.
In the second half, Oman continued to dominate as it scored two more goals. The goals came from Thamir al Zaabi in the 58th minute and Arshad al Alawi scored just seconds later.
Later Rasheed Jaber said, “We had many chances to score in this game. It was a good game for us. I think our players need to learn more.
“Overall, I am happy with the results because we are the only team who scored five goals against Nepal. Hopefully, we will have a chance to qualify for Indonesia as one of the best five runner-up teams. Otherwise, we will have to go back and build another team and build this team for the future too.”
Against UAE, Bahrain needed a win to pip Oman into second place in the group.
It was a goalless first half but Bahrain played with ten men after the 31st minute when defender Khalil Ibrahim al Balooshi was sent off for a second yellow card.
Bahrain took control of the match in the second period and finally found the net in the 73rd minute, with Ali Hasan Meftah the goalscorer.