Bruno Aires put the hosts ahead when he converted a penalty in the 41st minute, and the lead was doubled after Diomansy Kamara found the net in the 85th minute at the Indira Gandhi Stadium, which saw a turnout of over 15000.
While Northeast United FC jumped to the top four, the visitors, coming here after the 0-7 thrashing at the hands of FC Goa, are struggling at sixth place and will need to win their remaining games to harbor hopes of advancing to the next round.
The changes seemed early in the game for Mumbai City who showed composure and some good passing. In the first minute itself there was an opportunity for Saran Singh to open the account but Rehenesh proved equal to the task when Saran fired a volley.
NorthEast United were subdued for long spells but the hosts moved ahead in the 40th minute after they won a penalty. The dangerous Kamara controlled a ball on the left and then worked his way inside the danger zone where he collided after contact with Mumbai City defender Rowilson Rodrigues. The referee promptly awarded a penalty which Bruno Arias converted despite Mumbai City goalkeeper Subrata Paul diving in the same direction.
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Early in the second session, Anelka went close when he played a nice one-two with Chhetri and despite pressure from NorthEast defenders, controlled the ball well and shot at goal which was saved by Rehenesh.
Rehenesh was alert again in the 81st minute when Anelka seemed to have done enough to turn home Sony Norde's cross from the left but the goalkeeper managed to get a touch to the ball and push it away to safety.
India international Sunil Chhetri came agonisingly close to scoring for Mumbai City FC in the 74th minute but his left-footed effort missed the post by few inches.