Television microphones picked up the offending chants at Shielfield Park, forcing the host broadcaster to issue an apology.
And the Division Three club issued a statement even before the end of a 3-1 victory.
It read: "The club is disappointed by certain outbursts of inappropriate singing by a section of the support at Berwick.
"Our fans have been excellent this season both home and away and we do not want to see this tarnished."
Manager Ally McCoist said after the game: "I didn't know anything about it until I came in. Our supporters have been nothing short of sensational home and away this season. If they were a little bit out of order today, I apologise.
"We don't need it within the club or Scottish football. I'm very, very hopeful it's a one-off and won't happen again."
