Gurjant Singh (31st minute), Harmanpreet (34th) and Rupinder (46th) scored in the regulation time for India.
India came into the match as massive underdogs, but dominated most of the game.
The Indian team, due to their inconsistency, had finished the group stage at the bottom of Pool-B with 2 defeats and a draw from 3 games.
Earlier, India took the lead a minute after half-time.
India's show, perhaps, reflected in the way veteran striker SV Sunil upped his game in the first half, where he got to the end of two brilliant balls but was unfortunate to see his deflections go wide.
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However, as was the case in the match, India took the lead in the shootout but the world no. 3 Belgium fought back as the five-a-side chances ended in a score of 2-2 after goalie Akash Chikte blocked four Belgian attackers during the shootout, while Lalit Upadhyay, Rupinder Pal Singh were on the mark for India.
The hosts kept up the pressure and secured their first penalty corner in the fifth minute but Harmanpreet Singh's attempt was easily dealt by Belgium goalkeeper Vincent Vanasch. A quick change of passes helped them deal with Belgium's superiority on slick ball control and one-on-one advantage.
Instead, Belgium got what they desired.
Belgium Loick Luypaert is staking a claim to be the player of the tournament irrespective of where his team finishes.
The Belgians, ranked third in the world, however refused to cave in and hit back strongly to silence the crowd.
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Rupinder struck a few seconds later to revive India's lead, firing to the right corner of the goal-post. "Bring it on", Belgium coach Shane McLeod had said on the eve of India's quarter-final match against India.
Another opportunity visited India within four minutes: a penalty corner that resulted from a brilliant play by Birendra Lakra and Bikram Singh. But Karkera and his defensive set-up did their job to take the game to the shootout where Chikte emerged a hero. For Belgium, Arthur van Doren and Floren van Aubel hit the target. Chikte, who had stepped in after Luypaert's second goal, made a comfortable-looking save, but one that effectively made it easier for both teams to play for the shootout.
For India, Harmanpreet, Sumit and Akashdeep had failed in their strikes.
"It's a positive start".
"It was a really exciting game, I'd describe it as nail-biting", he said.
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The other match of the day saw defending champions Australia run out 4-1 winners against Spain, despite going 1-0 down in the 20th minute.