The Indian had pole position but engine issues forced him to pit early and re-join the race from the back of the field.
However, Karthikeyan worked his way to the podium behind winner Sergio Campana (Ibiza Racing Team) and second-placed Kevin Giovesi (Ghinzani Motorsport).
Karthikeyan helped his side Super Nova earn 15 points and kept them in the lead in the team championship.
"This podium finish definitely feels like a win for me. Despite the fact that we had scored the pole, I was forced back to the pit-lane due to a glitch in the acceleration system. Once back on-track, I caught the tail of the field and started to pass my opponents, also profiting from some contacts ahead. Now I'm aiming for the win in Race 2," Karthikeyan said.
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