By March 2001, Berger had recovered and he went on to feature in the final of both the UEFA Cup and the FA Cup, with Liverpool winning both trophies. In the 2001 FA Cup Final he provided the assist for Michael Owen to score the deciding goal against Arsenal. He appeared in the 2001 FA Charity Shield, coming on as a substitute as Liverpool won the competition. He then underwent knee surgery in August 2001, ruling him out of the 2001 UEFA Super Cup. Recurring injuries between 2001 and 2003 continued to disrupt Berger's career and deprived him of a presence in the first team, resulting in his decision to leave Liverpool after the expiration of his contract following the conclusion of the 2002–03 season. Berger had been confined to the bench for the duration of his final season when selected, limiting him to four appearances. He left Liverpool, having scored 35 goals during his seven seasons with the club. Newly promoted to the Premier League, Portsmouth manager Harry Redknapp signed Berger on a free transfer. Redknapp said of the deal: " a quality player, free – and the type of player who'll bring good experience to Portsmouth. I had a bit of competition for him but he's looked round the area and is very happy to join us." Berger made his first appearance for Portsmouth on the opening day against Aston Villa; he scored the club's second goal. Berger scored the winning goal in Portsmouth's victory over his former club Liverpool in October 2003. A month later, he set up the first and fourth Portsmouth goals and scored the fifth in Portsmouth's 6–1 win against Leeds United. On Boxing Day 2003, Berger helped Portsmouth to a 2–0 win against Tottenham Hotspur, scoring both goals of the match from free kicks, the first of which was scored from . Berger underwent an operation upon his knee in February 2004, forcing him to miss the remainder of the season. Berger started the 2004–05 season with note, scoring August's contender for Goal of the Season against Charlton Athletic. His second goal of the campaign came in a 3–1 win away to Crystal Palace, striking from . October 2004 saw his final league goal for Portsmouth in a 2–2 away draw at Norwich, scoring a 25-yard free kick. The club endured a difficult end to the season, winning just once in a period of 12 matches, which prompted the appointment of Alain Perrin as Portsmouth's new manager. Berger was one of a number of players including Steve Stone and Shaka Hislop whose contracts were due to expire in the summer.