Patel, who finished third in the 11th-leg yesterday at the same Buddh International Circuit where the F1 Indian GP was held, was ahead for a major part of the race and pipped to the post by South African rookie driver Aston Hare for the top spot. Malaysia's Daniel Hidzir finished third.
The Indian started fourth on the grid and worked his way up the ladder but failed to hold on to the challenge from Hare who began at third.
Fellow Indian Akhil Khushlani finished seventh while Raj Bharath and Vishnu Prasad ended ninth and 10th respectively.
Championship leader Nabil Jeffri started on pole but slipped down the order after being handed a drive through penalty for a false start infringement. Yesterday's race winner Afiq Ikhwan, who began in second position, finished fourth.
"It's a great feeling being on the podium here in front of my home crowd and to do it again today feels just brilliant," said Patel, who is the US Formula Project driver.
"It's such a hard race because on the first lap I fought with Nabil and Afiq. I managed to get past Afiq on turn 5, something I did not do yesterday. I realised last night what my mistake was and tried correcting it and it worked today and I got past Afiq there," he said.
"Afiq and Aston caught up with me in the slipstream and the race became a little bit tight. Fighting right through the race I ruined my tyres a bit early and I think after six laps I was sliding all over the place so it was really hard for me to keep Aston behind." MORE