Paul Le Guen's side topped the pool by two points from Jordan heading into the fixture at the Sultan Qaboos Sport Complex and goals from Amad Al Hosni, Qasim Said and Sami Al Hasani ensured Oman remained unbeaten during qualifying.
The hosts made the brighter start and Al Hosni fired the first warning shot on 13 minutes when he beat Shakir Hamzah in the air and headed narrowly wide.
There was no reprieve for Singapore four minutes later, however, as Al Hosni capitalised on a mistake from Safuwan Baharudin and, although his initial shot was saved, he blasted the rebound into the top corner.
Oman twice almost went into half-time with a two-goal cushion. First Eid Al-Farsi sprung the offside trap and fired a shot that rebounded off the post, before Al Hosni showed a piece of ingenuity with an overhead kick that cannoned against the crossbar.
Said did double Oman's advantage six minutes into the second half, angling a low shot that deflected into the back of the net with goalkeeper Hassan Sunny left flat-footed.
That advantage was further extended after 69 minutes, Al Hasani playing a neat one-two with Said and coolly finishing inside the box.
Singapore then gained a small consolation with 13 minutes remaining, as Shahril Ishak slotted underneath the legs of Ali Al-Habsi, the first time that Oman have conceded in qualifying.
Oman now return to the Asian Cup, which will be held in Australia next year, after missing the 2011 edition in Qatar, while Singapore finish bottom of the group with just three points.
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