The Irish midfielder was shown a red card by referee Alan Muir during the first half of Saturday's goalless draw at Easter Road, just 34 seconds after replacing the injured Murray Davidson.
But the Perth outfit say they intend to challenge the red card and have now written to the Scottish Football Association to lodge their protest.
A statement on the club's official website said: "Saints have today lodged an appeal with the SFA against Paddy Cregg's dismissal in Saturday's game against Hibernian.
"The midfielder was red carded by Muir within a minute of him replacing the injured Murray Davidson in the 30th minute of the match."
Cregg's quickfire sending off came just seven days after striker Rory Fallon was also shown a straight red card after only 51 seconds after coming on as a substitute in their 2-0 defeat against Aberdeen.