While Chatterjee won the first race of the day with a victory margin of more than five seconds, the win in race two was much sweeter as it came after a hard battle with Shanmugam, who had won both the races yesterday.
Shanmugam settled for second place while Dhruv Mohite was a distant third.
With the double today, Mumbai-based Chatterjee has extended his lead in the Championship. The 18-year-old had also won both the races on Sunday in the first round held in July at the same venue.
High on confidence, he later revealed that he had secured a drive in the Formula Masters China for the 2017 season.
"We struck the deal last week. Now really looking forward to some testing in November. I had earlier planned to go to the UK but it was turning out very expensive. I am glad this deal (in China) went through. Big thanks to JK Tyre for that," he said of the single seater championship.
It was an action packed race as a safety car had to be called following a collision with Akash Gowda and Karthik Tharani, who eventually failed to finish.
Results:
Euro JK 16: Race 3: 1) Nayan Chatterjee 2) Ajay Kini 3) Ananth Shanmugam
Race 4: 1) Nayan Chatterjee 2) Ananth Shanmugam 3) Dhruv Mohite
Formula LGB 4: Race 2: Ashwin Sundar 2) Raghul Rangasamy 3) Vishnu Prasad
Race 3: 1) Vishnu Prasad, Raghul Rangasamy 3) Rohit Khanna.
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