Karthikeyan, who had won Race 1 at Silverstone from pole position last month, set a scorching lap time of 1:34.583 to claim pole yet again for his side, Super Nova International.
The Indian pipped Kevin Giovesi of team Ghinzani Motorsport by 0.035 seconds.
Karthikeyan's Super Nova teammate Vittorio Ghirelli was third fastest with 1:34.757.
Race one will be held later today while race two will be held tomorrow.
Championship leader Kimiya Sato will start fifth for Euronova and former Grand Prix driver Christian Klien tenth for Zele Racing, Karthikeyan's team earlier in the season.