In a thrilling 36-hole final, the two youngsters matched stroke by stroke.
Shubhankar made five birdies, while Viraj fired four with the former returning a gross score of 3-under par while the latter was 1-under at the breather (18 holes).
After the break, Viraj birdied the 20th hole to further reduce the margin to 2-down.
In a see-saw battle, Shubhankar birdied the 22nd hole (4th hole of the course) to regain the 3-up advantage.
By the 31st hole, the fighting Viraj fired two birdies and reduced the margin to 1-down.
However, Shubhankar made two consecutive birdies on the 32nd and 33rd holes, respectively as Viraj managed pars to take a 3-up lead with three holes to go.
Both halved the next hole with pars as Shubhankar dashed the hopes of 15-year-old to become both junior and senior champions.
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"It is an amazing feeling to win the biggest and most prestigious tournament," the 16-year-old said after recording his first victory on the IGU Amateur Tour.
"It is a mixed feeling. I won the title, but my heart goes out to Viraj who is a very dear friend of mine. He made a superb comeback in the last 18 but the birdies on the 14th and 15th sealed the issue," he signed off.