The home team completed a cup double over Saints taking their place in the next round of The Scottish Junior and Fife & Lothian Cups.
Ground conditions were poor after three home games in a row for Arniston but as they say, it’s the same for both clubs.
Before Saints could blink, Arniston scored straight from kick off with an early ball forward to Watson and he chanced his luck with a lob which flew over keeper Hunter high into the net.
Saints were stunned and took time to recover.
Play on the surface was difficult and Saints tried to adapt with longer passes.
It looked after 15 minutes play, that an equalising goal would be a while in coming but defender Graham decided to have a go from 25 yards in 17 minutes and his well hit left foot shot was too good for Cornet as it passed him into the top corner.
Saints looked better now and for several minutes worried the defence of Arniston without having a proper chance to score.
In 21 minutes hesitation by Saints and an intercepted short pass in midfield saw the home team break through with players forward and Hay hit a very well placed shot past Hunter for the lead again.
On the half hour, further problems for Saints when Fleming received a second yellow and sent off for alleged abusive language directed at the ref.
A shot from Arniston in 53 minutes was hit high and wild and a great chance to increase their lead was lost.
In 62 minutes substitute Anthony came on for Falconer.
Two minutes later Saints looked to have the makings of attacking play but from 30 yards McInnes decided to have a shot but his effort was well off target and over the bar.
Arniston looked as if they would sew the game up in 69 minutes when a forward broke clear into the area but Saints defence recovered to force it away for a corner.
With Saints pushing forward trying for an equaliser, Arniston broke up the left in 71 minutes but their final effort was just wide.
The home team defended deep and held onto their lead.