Karthikeyan, who battled with engine problems all weekend, gained two places in the 35-lap race to claim his first points of the season.
The former Formula 1 driver had finished seventh in the 25-lap sprint race in the morning after starting ninth on the grid. He was forced to retire in the season opener at Suzuka last month.
His teammate at Team Lenovo Impul, JP de Oliveira from Brazil, won the first race from pole position before he held on to second place in the afternoon.
Karthikeyan, who did a Formula Nippon (now Super Formula) season way back in 2001, said he has lots to learn about the tracks and conditions in Japan before he can be a regular podium contender.
"It was a tough weekend starting from practice, where I suffered a tyre failure. The loss of 20 minutes due to an engine problem cost me valuable track time in second practice. I could not improve much in the races for the surprising lack of straight line speed," said Karthikeyan, who collected four points from the double header, referring to the change in engine from the last round where he had qualified on the front row.