After being kicked by Joachim Löw, Scharner transferred to relegation battler SV Salzburg in January to help them for the rest of the season. He made a total of 13 league games for Salzburg that season, 4 of which were won and three tied, scoring two goals, against Wacker Mödling and Bregenz, respectiveley. He saw his first yellow/red card in a 3:2 win against Kärnten, the same site that kicked Salzburg out of the 1/8 finale in the ÖFB-Cup, sweeping them 4:0. He collected a total of five yellow cards that season. The team managed to avoid relegation at the end of the season.