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Chatterjee started the first of the two races from the front-row and passed Sohil Shah for the lead on lap 2, but the pole-sitter fought back to reclaim the spot a few corners later.
That was as far as their battle went, Shah coming into the pits to serve a drive through penalty for a jump start.
Shah's penalty released Chatterjee in clean air and the Mumbai-based driver took full advantage of the situation to romp to his third victory of 2019.
Nirmal Umashankar finished over two seconds adrift in second, with A Bala Prasath claiming the final podium spot in third.
Yash Aradhya, who is also competing in F4 SEA this weekend, was classified fifth, ahead of Vishnu Prasad.
Photo by: Srinivasa Krishnan
Multiple national-level champion Prasad started third in the partially-reversed race 2 but moved into the lead on the opening lap to score a victory on his return to MRF F1600 series.
Rupesh Ravikumar made a slow getaway from pole position, allowing Raghul Rangasamy to take the lead heading into turn 1.
Prasad and Sandeep Kumar also managed to dispatch Ravikumar a few corners later, before latching onto the back of Rangasamy.
By the end of the first lap, Prasad had passed Rangasamy for the lead of the race - a position he would hold until the end of the eight-lap encounter.
Sandeep Kumar later overtook Rangasamy to snatch second, with pole-sitter Rupesh settling for fourth.
Aradhya was fifth while Chatterjee was unable to make much headways from his starting position, ending up sixth at the flag.
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