Jagan clocked a best lap time of 2:03.253, while Deepak had a fastest timing of 2:03.835 under wet conditions at the Sentul International Circuit which was lashed by rain just before the start of the qualifying race.
25-year-old Jagan was occupying ninth position before he did his best lap time in his 10th and final lap. He will start at the second row in the grid in the final race tomorrow, while 27-year-old Deepak will be at the third row.
The top three in today's qualifying -- Rheza Danica (Indonesia), Ahmad Syukran bin Mohd Yusof (Malaysia) and Handy Tuahatu (Indonesia) -- will start in the first row.
It was, however, a bad day for Rajini Krishnan in the ST 250 class, the lone Indian in the fray in that category, as he could barely complete a lap before his bike developed a problem in Electronic Control Unit (ECU). He will start at the back in the fifth and last row in the final race tomorrow.
An upbeat Jagan said he would look for a podium finish.
"We have a chance to be at the podium tomorrow. I am happy about my position at the qualifying today and will do my best tomorrow," Jagan said after his race.
"It was a wet track but I have raced under similar conditions earlier. So, I was not worried about it," Jagan, who had finished second in Japan in 2012 as the best in his career, said.
