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Shafeel scored the winner in the 67th minute as Services won the final 1-0 to lift their seventh Santosh Trophy.
Services shot into lead through a left-footer by Keralite Rahul Ramakrishnan in the 21st minute.
After 120 minutes of goalless action, both sides converted most of their kicks, but Kerala's substitute Sujith V R missed the decisive one.
Manipur will meet Goa in the second semifinal on Thursday (7 pm).
Services will take on the winners of Tuesday's Mizoram-Kerala quarterfinal for a place in the summit clash.
The match will kickoff at 7 pm on March 5.
Kerala will meet the second-placed team from Group B in the fourth quarterfinal on Tuesday (7 pm).
Services outplayed Assam 2-0 in the early kick-off to seal their place in the quarterfinals.
Kerala, who beat Assam 3-1 in their opening match before going down 0-2 to Goa, have four points from three games.
This was Karnataka's second consecutive draw after a 1-1 result against Delhi.