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The young racer clocked the fastest time of 1:03.827 to finish on pole while his nearest rival, Chetan Korada was 0.430s away.
Parekh was fast all through the session and was the only driver to dip under the one minute and four-second barrier.
Championship rival Arjun Narendran missed on the front row and slotted in at third.
In fourth was Tejas Ram who pushed championship leader Karthik Tharani to fifth while newcomer Anindith Reddy qualified sixth ahead of South Indian actor/racer Jai Sampath in seventh.
The top 10 was rounded off by Anshul Shah at eighth, Aayush Soni ninth and Hamish Robinson at tenth.
Earlier in the day, the drivers got a proper dry run in Free Practice 1 with Tharani leading Parekh and Narendran.
All set for Round 3 of MRF 1600 championship
Parekh elated to be on pole at Coimbatore