Tom Sharples was a four-goal hero for Ruthin, scoring on 26, 79, 83 and 90 minutes for the hosts, with Warren Aykroyd-Duckett also on the mark.
Andy Booker had earlier edged Rhydymwyn in front from a second-minute spot-kick.
Sharples equalised before half time, but a Gary McConnell goal on 53 put Rhyd ahead again.
However, Ruthin had the staying power to add four more to their tally in the last 17 minutes to seal the tie.
White Bear advanced to the next round of the North East Wales Football League Vets Cup with a 5-1 triumph at Shotton.
Ross Gilbert put Buckley ahead in just the third minute, but a Ryan Dunn penalty in first half stoppage time made it level at the break.
Bear took command in the second half, Dunn adding a second before Dave Littler made it 3-1 on the hour.
Gareth Roberts and Paul Morgan notched further away goals before the end.
Gareth Williams and Michael Pritchard scored two apiece as unbeaten leaders Llay moved four points clear at the summit.
Williams and Pritchard both produced first-half doubles to give Jonny Taylor’s side a comfortable 4-0 interval lead.
Steve Evans, Ian Williams and Darren Pritchard provided assists.
No further goals arrived until the 77th minute when Peter Williams pulled one back for Phoenix.
Any thoughts of a dramatic recovery were ruined for the visitors when Kerry Howells almost immediately made it 5-1.
Karl Rowlands bagged a late consolation second for Pen.
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