Kalu Uche (6') opened the scoring for Delhi but a brace from Willis Plaza (35', 106') sealed Churchill's progression into the Round of 16.
Delhi Dynamos made three changes to their side from their last Indian Super League (ISL) game against FC Pune City. Xabier Irureta returned under the sticks replacing Arnab Das Sharma. Pritam Kotal came back to occupy his usual position on the right side of the defence. Sajid Dhot and Gabriel Cichero paired up as the two centre backs with Munmun Lugun as a left back. Paulinho Dias and Matias Mirabaje shouldered the responsibility in midfield with Nandha Kumar and Romeo Fernandes playing as wide midfielders. Kalu Uche led the attack upfront.
Alfred Fernandes also made three changes to the starting XI that suffered a 1-0 loss to Minerva Punjab. Jovel Martins, Bektur Uulu and Nicholas Fernandes made their way into the lineup at the expense of Israil Gurung, Francis Okechukwu and Visalie Mezhu.
The game got off to a flying start as a blinding effort from Uche gave Delhi the lead as early as in the sixth minute. The Nigerian opened up space for him with a body feint and his shot caught the goalkeeper off his line and the ball went through the legs of Osagie Monday to nestle inside the net.
The early goal took the sting out of Churchill's performance as they kept ball-watching, giving ample time for Delhi midfielders to control play at the centre of the park.
Churchill tried to make use of the wings to slowly get back into the game. Britto got some opportunities to swing in some crosses from the right but his deliveries were not up to the mark to trouble Xabier.
Nandhakumar on the left was the livewire for Delhi as he provided a steady supply of crosses into the box, keeping Monday on his toes for the most of the first-half.
Just after the half-hour mark, Nicholas found the back of the net completing a fantastic build-up which was started by Ceesay, constructed by Plaza and then finished by Nicholas. But the referee on the sidelines held his flag up as the Goan winger was a yard or two offside when the ball was played to him.
Cardozo was once again called to action when Mirabaje found an over-lapping Kotal inside the box with a perfect diagonal delivery. The right-back set himself up with a fantastic first touch but rifled his shot straight at the keeper.
Churchill fought back into the game with an equaliser from Plaza on the 35th minute. It was another inch-perfect cross from Nicholas which found an onrushing Plaza. The Trinidadian controlled the ball with an exquisite first touch and triggered a shot which went into the net after touching the inside of the near post.
Chhangte tried his luck from distance but to no avail as Churchill began defending in numbers so that they could head to the tunnel with the scores level at 1-1.
Both coaches played their cards after the break as Seityasen Singh joined the action whereas Israil Gurung came off the bench for Churchill Brothers.
The first goalscoring opportunity fell for Delhi within ten minutes of resumption when Mirabaje spurt out a defense-splitting through ball for Seityasen. If the substitute had reacted a fraction earlier in a one-on-one situation with Cardozo, Delhi could have gone up 2-1 up. But, a second's delay allowed Monday to block the shot.
Both teams started moving out of their defensive shell in search of goal which opened up spaces on the back. Plaza started troubling Delhi's defence with his tricks and forced a two-handed save from Xabier.
Churchill started lumping the ball forward in search of Plaza and Ceesay, whereas Delhi tried to regain control of midfield by bringing on Vinit Rai.
If Plaza had managed to just guide his header into the net after latching onto a cross from Ceesay, the Goan side could have gone ahead in the tie. His poor header from sniffing distance of goal brought back the memories of his days with East Bengal.
It was end-to-end stuff, as minutes later Uche found the net once again but Kotal was deemed to be in an offside position when he received the ball on the right flank before passing it to Uche.
Chances fell thick and fast for Delhi, but the capital-based side could not make them count. It was Chhangte once again who failed to direct his shot into the net even after he was set up on a platter by Seityasen. Uche tested Cardozo with a shot from the outside of his boot which was finally cleared away by Eldor. He pulled his hamstring while positioning himself to shoot which prevented him from taking any meaningful part in the play, although the striker continued on the pitch.
It was all square at the end of regulation time and the teams headed for extra-time in search of the winner.
Delhi started on the front-foot with their short passing game in their bid to break down Churchill's defence. The relegated I-League side was happy to sit back and formed two lines of defence in front of Cardozo to deny space to the opposition.
Plaza could have scored his second after a fantastic combination play with Ceesay but the forward's curling effort was just wide of the far post.
The first-half of extra time was not enough to break the deadlock as although Delhi had possession with them, they failed to make it count.
Churchill have a penchant for scoring late goals as evidenced in the I-League where they scored 11 goals in the final 15 minutes. And they managed to go in front within the first minute of the second-half of extra time when a long ball from Meitei was brilliantly brought down by Plaza, who kept his composure to calmly slot it past Xabier.
Delhi Dynamos showed a sense of urgency after conceding but a resolute Churchill defence would not be breached the remaining minutes.
With this defeat Delhi Dynamos crash out of the inaugural edition of Super Cup whereas, Churchill Brothers progress to the next round to take on Mohun Bagan on April 1, 2018.