FC Goa returned the favour just four minutes later when Seriton Fernandes and Alberto Noguera played a quick one-two, before sending the former free on the right flank.
Bartholomew Obgeche (20th minute) gave the hosts early lead before Farukh Chaudhary cancelled out his strike in the 49th minute.
Just as BFC looked set for a win, Machado (78th) struck again to ensure his team got a point.
Bagan adopted a completely different approach from the first leg. They had 16 shots in the first half but just three on target. It took them just three minutes to sound a warning.
Chennaiyin FC bounced back from a losing start in Indian Super League season 4 as they beat North East United FC 3-0 at the Jawaharlal Nehru Stadium in Chennai on Thursday.
Indian Super League franchise NorthEast United FC (NEUFC) co-owner John Abraham expressed optimism that the country's ranking in international football would go up to 'double digit' from the current 159th position in the next seven years.
Both sides created chances in the first half but it was SCEB who converted them and deservedly headed into the break with a two-goal cushion.
North East United FC (NEUFC) and FC Pune City (FPC) missed a lot of scoring opportunities as their Hero Indian Super League match ended in goalless draw in Guwahati on Saturday.
An entertaining 11 minutes ensued with four goals, two at either end. First up, Brazilian target man Silva made most of Udanta Singh's build-up play, to leave NorthEast defenders high and dry with a fine goal.
Bollywood actor John Abraham, also the owner of NorthEast United Football Club (NEUFC), called on Assam Chief Minister Sarbananda Sonowal and discussed with him issues related to the opening ceremony of the third edition of Indian Sports League (ISL) in Guwahati. The Chief Minister and the Bollywood actor discussed last evening the measures being taken to make the opening ceremony a success, an official release said on Wednesday.
The result also meant Khalid Jamil is still unbeaten in the competition and extended NorthEast's winning run to ten games.
ATK earn a dramatic 1-0 win over NorthEast United FC and reclaim the top spot
The result means Mumbai sit at the top of the pile with 16 points from eight games but have drawn after their 0-3 loss to Kerala Blasters. NorthEast United remain ninth having eight points from nine games.
Khalid Jamil also created history by becoming the first Indian to coach three or more league games and guide a side to the playoffs.
The home side, who kicked off the fifth ISL season with a 0-2 loss to Kerala Blasters, were reduced to 10 players in the 32nd minute when Sena Ralte was sent off for a sloppy challenge.
NorthEast United got the better of Mumbai City yet again, doing a double over the Islanders with a 2-1 win in the Hero Indian Super League
But the hosts did have their equaliser in the 54th minute from another corner. Rene Mihelic whipped one into the far post where Rana Gharami managed to head it back across the box. Kotal, this time around, directed it home from close-range.
Many Indian footballers have improved by leaps and bounds thanks to the exposure of playing in the Indian Super League in the last three seasons.
News of all that's transpired on and off the football field
North East United FC had a pretty forgettable inaugural season, but they look to make amends in the second edition of the Indian Super League.
Former Manchester United star and Indian Super League side ATK's coach Teddy Sheringham said it was unusual to finish a football game post midnight, something that he had never experienced in his long association with the game.
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