The 2008–09 season did not start well for Seitaridis, as he lost his place in the first team to new signings Tomáš Ujfaluši and John Heitinga, and his heavy contract meant that Atlético was looking to sell him. Despite that, Seitaridis was a starter in Atlético's opening game, in a 4–0 victory over Málaga CF, and went on to make 14 league appearances that season. On 29 April 2009 however, him and teammate Maniche were suspended by Atlético's president Enrique Cerezo because they failed to appear in an Atlético home match against Sporting Gijón despite not being included in the 18-man squad. Two weeks later on 13 May 2009, it was announced that Seitaridis was released by Atlético a year before his contract was to expire, with a statement on the club's official website reading "Seitaridis is therefore free to negotiate with other clubs who may be interested in signing him".
On 10 September 2009, the last day of the Greek transfer period for free agent players, Seitaridis signed a 4-year deal with Panathinaikos, returning to the team after five years. It soon became apparent that Giourkas was unfit and was struggling to re-establish himself due to frequent injuries, missing most of the 2009–10 season's matches. However, on 21 March 2010, he surprisingly returned to the line-up for the big derby against rivals Olympiacos, and despite their defeat, Panathinaikos managed to end the season positively by winning the double. Seitaridis himself didn't appear at the 2009–10 Greek Cup final against Aris Thessaloniki due to injury, but made 2 appearances on the road to the final.