Delhi's Shamim Khan, the 2017 PGTI Order of Merit champion, returned a card of six-under-64, to be second.
Thangaraja, runner-up at the PGTI event in Hyderabad last week, dominated the opening round with a breathtaking nine-under-61 that featured an eagle, eight birdies and a bogey.
It was the joint best round of the Sri Lankan golfer's career that gave him a handy three-shot lead.
Thangaraja, apparently eager to make up for missing the cut at the previous edition of the Chennai Open in 2016, looked in good form from the start.
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"It's just been an unbelievable day. It is only the third time I've shot a nine-under. This is my lowest round on the PGTI. My hitting was outstanding, especially my driving," said Thangaraja, who participated in the 2010 Asian Games.
Shamim Khan benefitted from a hot putter en route his 64. He drained a number of putts from 12 to 15 feet as he stitched together eight birdies at the expense of two bogeys.
Defending champion Mukesh Kumar of Mhow was in tied third place with a round of four-under-66.
Twenty-one-year old rookie Shivnaren Srinivasan of Chennai, playing at his home course, fired an even-par-70 to be the highest placed among the six Tamil Nadu-based golfers, at tied 26th.