Thirty-six-year-old Shankar took his three-day total to 12-under-204 ahead of the final round.
Greater Noida's Sudhir Sharma, who was overnight tied fourth along with Shankar after setting a new course record on Wednesday, also moved up two spots in the penultimate round. Sudhir's 69 on Thursday placed him second at 11-under-205.
Bengaluru's Trishul Chinnappa, the halfway leader, slipped to tied third as a result of his third round of 73. Chinnappa shared third place with Noida's Gaurav Pratap Singh (71) at nine-under-207.
Panchkula's Angad Cheema was the highest placed among the Tricity golfers. Cheema (68) closed the day in tied 12th at five-under-211.
The conditions during round three were unforgiving as it was the windiest day of the tournament and the breeze kept switching directions. The tough scoring conditions meant that only 17 players out of a total of 57 could break par on day three.
Shankar (68-68-68), a seven-time winner on the PGTI, negotiated the conditions well to shoot the day's joint best score and keep his card bogey-free. He struggled to find greens in regulation but more than made up for that with his fine chipping and putting.
The 2014 TATA Steel PGTI Order of Merit champion made a couple of chip-putt birdies on the second and 16th and landed his wedge shots within six feet for birdies on the sixth and 18th.
The man with three top-10s this year will now be looking for his first win since September 2017.
Patna's Aman Raj and Bangladesh's Md Dulal Hossain, who were both overnight tied second, shot identical scores of 74 in round three and thus dropped to tied fifth at seven-under-209.
Jyoti Randhawa was in tied 29th at one-under-215.
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