The Red Machines finished on top of the group with three straight wins and will face either Salgaocar FC or Mohun Bagan in the semi-finals
Anthony Wolfe (8', 73') and Gabriel Fernandes (19', 53') scored a brace each for Churchill and Pune respectively while Lenny Rodrigues scored in the 32nd minute for the winners.
Marinao Dias started with Ravanan Dharmaraj and Thangjam Saran Singh on the bench in favour of Naveen Sudhakaran and Bineesh Balan who earned their first starts in the tournament.
Mike Snoei meanwhile made three changes from his side that lost to United SC, handing on-loan player Gabriel Fernandes his first start besides opting for Dhanpal Ganeshan and Zeeshan Rahman while Othallo Tabia, Arata Izumi and Mumtaz Akhtar were benched.
Both sides dragged shots wide before Abdelhamid Shabana got past Calum Angus to put in an inch perfect cross for Anthony Wolfe who scores his first goal for Churchill Brothers in the eight minute.
James Meyer set up Anthony D'Souza on the left, whose attempt to find the far post saw Churchill goalkeeper Lalit Thapa spill the ball and Gabriel Fernandes latched on to the rebound to score the equalizer in the 19th minute.
Minutes later, Gabriel almost completed his brace if not for a block by Sanjay Balmuchu after the former received a good cross by Anas Edathodika from the right.
Two minutes after the half-hour mark, Wolfe set up Lenny Rodrigues on the left who blasted his shot past Pune FC goalkeeper Amrinder Singh to restore his side's lead.
In the 40th minute, Pierre almost set up rival player Shabana in his own half, while the Egyptian managed to get past Angus but chose to go for goal and failed to find the target instead of passing to Balwant.
Pune FC had a chance to equalise once again just before half-time as Riga whipped the ball right across the face of the goal but Gabriel directed it just wide of the far post.
The Red Lizards scored the equaliser for a second time in the 53rd minute after Dhanpal Ganeshan's shot from midfield struck a Churchill defender and only Gabriel was swift to react as he whacked it past Thapa.
Three minute later, Ganeshan almost scored a goal of his own when his well directed header from a D'Souza cross came off the crossbar.
Wolfe also saw his shot strike the crossbar after being found in the box by Balwant in the 71st minute before he scored the winner two minutes later.
The former Trinidad and Tobago international coasted in behind Angus to receive a cross by Balwant before evading Amrinder and finding the back of the net.
Balwant's attempt to increase the tally for Churchill Brothers resulted in his shot missing the left post by a whisker while Pune FC failed to make any more in-roads in attack.
Snoei's men finished their forgettable campaign in the cup competition winless as they now shift their focus to the I-League in which they are currently placed third.
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