Shiva Shrestha scored the opening goal for Nepal connecting a well timed one-to-one pass from skipper Nirajan Malla in the first half while Jagjeet Shrestha sealed the win after Solo of Peerless had equalised in the injury time of the first half.
ANFA will now face the winner of the game between Assam State Electricity Board and Amity United Haryana.
Backed up by a sizeable number of Nepali supporters, ANFA failed to strike a cord up front in the opening minutes of the game. They seldom created any chances, losing possession rather easily against the physically superior Kolkota-based outfit.
Shiva Shrestha broke the deadlock in the 28th minute placing his shot in the right hand corner of the post from outside the D-box after playing a lovely one-to-one pass with skipper Malla.
Rohit Chand, who was called by the national team a few days earlier, was the heart of the defense thwarting most of the opponents' easy chance. Chand also had his role up front, creating a couple of chances. He fed an easy chance to Sujal Shrestha five minutes from the first half but Shreshta missed it while trying for a bicycle kick.
Peerless Club found the equalizer in the dying minutes of the injury time through Solo's header from close range from a free kick.
ANFA lost rhythm in the second half, lighting the rather dull first forty five minutes. Rohit Chand had his free-kick denied by the cross bar just after the interval.
Jagjeet Shrestha then had his long-ranger denied by his team mate in the 60th minute. Shrestha's shot was on its way towards the goal but deflected off the legs of Shiva Shrestha in front of the goal mouth.
Shrestha, however, found the winning goal nine minutes from time, through a shot that echoed from the upright. The goal came from the quickest of sequences, involving four players. Goalkeeper Dinesh Thapa served the ball to Ganesh Khadka, who fed to Nirajan, and his shot deflected off the post to find Shreshta, who slotted home from close range sending the sizable Nepali supporters into a frenzy.
ANFA boss Kishor KC expressed his happiness from the performance of the players saying the opponents were physically superior but we were technically strong. " We won the game because of our technical game. The hot weather spoilt out game in the first half," said K.C.