Shipperley was signed for Southampton by Alan Ball for a record fee of £1.25 million on 6 January 1995. New manager Graeme Souness signed Norwegian Egil Østenstad, prompting Shipperley to drop to the First Division by signing for Crystal Palace for a £1 million fee in October 1996. He scored 13 times for the Eagles over the rest of the season as the were promoted via the play-offs, including one on 10 May in a 3–1 home win over Wolverhampton Wanderers in the first leg of the semi-finals. In 1997–98, he scored seven times – including five consecutive games from October to December – in a season that ended with relegation.