After a goalless first half Oak went on to win despite being reduced to 10 men.
Josh Brown and Marcus Scott put the hosts two-up before they had a man sent off.
Oak are now just three points behind leaders Conwy Comrades with a game in hand.
Wanderers had to forfeit an away trip to Conwy.
A club spokesman said: “We originally thought we had a free week but were given a fixture early in the week, Unfortunately, we couldn’t field a team due to most of the squad being away or taking extra shifts at work.
“We’re set to be fined and deducted 3 points, but we are considering an appeal as we’ve worked hard for the points.”
Maxie Williams hit four goals for the visitors, who ran up double figures in a cup clash at Rhyl.
Oliver Carey netted three, Harry Kirkham and Tyler Griffiths two apiece and Dion Lloyd a single.
Royal Oak v Conwy Comrades
Rhyl Rangers v FC Mally
Y Clwb v Prestatyn Wanderers
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