Danny Davies’ first half header was enough to put the Saints into the final where they will face Penybont for a chance to complete a double - after wrapping up the title last week.
Bay, managed by former Saint Steve Evans, pushed Limbrick’s men all the way - but the Australian coach was less than impressed with the state of the Belle Vue pitch in the last four clash.
He said: “It hasn’t been a bad week for us.
“We knew what the game was going to be like today, I thought the pitch was difficult to play on, no disrespect to Rhyl at all, but the fact this semi final can be played on a pitch like this is unbelievable.
“But we had to grind it out and show a different side, a side that we have shown in recent weeks.
“You look at the scoreline and some will say we should be doing better but I disagree - they are an excellent side.
“They put it on us for the whole game and we’re just pleased to get to the final.”
The Saints will now take on Penybont in what should be a tight final - with the South Walians currently fighting it out in the Cymru Premier top four.
Limbrick added: “It is going to be a cracking final, they are an excellent side.
“We’ve drawn 1-1, won 3-2 and drawn 3-3, so hopefully there won’t be as many goals in this one.
“We’re looking forward to it, it was our target at the start of the season so we’re pleased to get there.”