Despite their unbeaten campaign, the Kolkata outfit exit the competition on goal difference as they played out a drab goalless draw against the Goan side.
Arthur Papas made four changes to his side from the last match with Peter Carvalho, Romeo Fernandes, Debabrata Roy and Jeje Lalpekhlua all getting back to first-team action at the expense of Prabir Das, Holicharan Narzary, Alwyn George and Tolgay Ozbey.
Sanjoy Sen also made a couple of changes to the starting line-up as Rakesh Masih and Jerry Zirsanga got the nod with Anthony Soren and Ashim Biswas making way for them.
Right from the onset, both teams showed plenty of attacking intent. In the third minute, Josimar Da Silva, the Brazilian striker of the Black and Whites showed good skill on the ball to get the better of Dempo's Haroon Amiri, but failed to put a cross into the box.
The forward was once again at the thick of things a few minutes later when he linked up perfectly with Penn Orji and claimed a corner kick but the tame delivery was of little help to the team's cause.
Dempo created their first goal-mouth opening move in the 14th minute, when Roberto Silva sent in a venomous corner but Romeo Fernandes was a bit late to slide in for the ball at the far post and his shot went just wide of the Mohammedan goal.
The match was only 15 minutes old when Sanjoy Sen, the Mohammedan gaffer, used his first substitution as the veteran Ashim Biswas was introduced with Jerry Zirsanga making way for him.
In the 18th minute, Dempo was once again close to scoring when Clifford Miranda sent in a good cross from the flanks for Jeje Lalpekhlua, but the 'AIFF Emerging Player of the year' was just a fraction of a second late to begin his run and failed to get to the ball.
In the 26th minute, Clifford's freekick from the right came off Mohammedan bodies but only as far as Pronoy who tried his luck from 25 yards, however his ambitious effort went just inches wide of the goal.
Four minutes later, Haroon Amiri darted inside rival territory from his own half but a timely interception by Luciano Sobrosa helped the Kolkata side to avert the danger.
Late into the first half, Penn Orji and Rakesh Masih both attempted long-range efforts but neither were enough to break the deadlock and the teams went into the break after a half that saw Dempo having the better share of possession.
In the second half, Mohammedan looked like a team on a mission as they employed a high defense line and looked sharper while going forward. In the 53rd minute, Penn Orji pulled the trigger from 25 yards after some brilliant work by Nabi, but his right-footed effort went just over the crossbar.
In the 59th minute, Josimar headed Penn in the clear but the ball bounced awkwardly off the Manjeri turf, making it difficult for the Nigerian to tap it in.
Seven minutes later, Simon Colosimo made a brilliant last-ditch tackle to stop Josimar from taking a shot, as the latter looked all set to to test the Dempo custodian from close range.
However, the best chance for the century-old Kolkata club came in the 73rd minute, when Syed Rahim Nabi sent in a pinpoint cross from the left flank for Josimar, but Laxmikant Kattimani was alert enough to parry away the header.
In the 89th minute, Jeje tried to befool Luis Barreto with an overhead shot, but his effort went over the crossbar. This was the last good move in the match and the runners-up of last year's competition held firm and secured a semi-final spot.
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