Sunil Chhetri scored a brace for Bengaluru FC to sink Pune 2-1 and carry English coach Ashley Westwood's boys into the semi-finals while strikes from Clifford Miranda and Romeo Fernandez helped Dempo beat Mumbai FC 2-0 and seal their berth in the playoffs.
Going into the Group B encounter at Vasco, Bengaluru needed a stalemate to secure a place in the playoffs, but they went one step extra to become the first team to reach the pre-summit round.
A lacklustre first half was set ablaze in the last three minutes with two goals.
The first was a screamer from Chhetri, when he acrobatically volleyed home after the ball came off Englishman John Johnson's head and fell perfectly in the path of the prolific forward.
Just when Bengaluru thought they had the vital goal to be happy at half time, they earned a second.
A few exchanges in the Bengaluru half later, Eugeneson Lyngdoh sent a perfect pass for Australian Sean Rooney who was through on goal.
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Amrinder Singh, the Pune custodian, however caught the Aussie's foot in the box.
Referee C.R. Srikrishna pointed to the spot and Chhetri scored his fourth of the tournament, putting it beyond the keeper whose correct guess was redundant.
Thongkosiem Haokip's header - four minutes from time - pulled a goal back for Pune.
It was Miranda's finish that gave Dempo an early lead in the 13th minute of the Group A encounter at Margao. Fernandez's corner found Aussie striker Tolgay Ozbey whose mistimed shot fell to Miranda who nodded the ball into the back of the net.
Dempo then heaped on the pressure and doubleD their lead after winger Holicharan Narzary found fellow medio Lenny Rodrigues, whose shot ricocheted off a rival defender and fell for Fernandez who rammed the ball into the net.
Mumbai FC tried hard to post a come back after the break but fell short with their best two chances coming in the last five minutes. First substitute Reisangmi Vashum acrobatically volleyed goalwards only to be denied by an in-form Dempo goalie Laxmikant Kattimani, and minutes later Sampath Kuttymani's snapshot with the outside of his right foot flew inches wide.
Courtesy the result, Dempo made through to the semis with a match in hand while Mumbai FC bowed out of the competition finishing their group matches with four points from as many matches.
Whoever wins Tuesday's crunch tie between East Bengal (4) and Sporting Clube de Goa (3) will join Dempo in the last four stage. The other team in the open group, Royal Wahingdoh, can outjump others to make the cut only if they can beat Dempo and hope that Sporting and East Bengal play out a stalemate.