The Uruguayan striker scored once in each session as the hosts surged to the top of the table with six points from their first two matches at home.
Both teams were cagey at the start and took time to ascertain each other's strength and spot weakness. NorthEast seemed more settled at the start and wasted a golden chance in the 12th minute.
A left-footed cross from Koffi Christian, popularly known as Romaric, was missed at the first post by Alfaro but there was still a chance for Yusa Katsumi who chose to go for glory himself, only for Goa goalkeeper Kattimani to make a diving safe.
NorthEast did not have to wait for too long for the opening goal which was a gift from the goalkeeper. Captain Lucio's back-pass for the Goa goalkeeper should have been routine clearance but instead Kattimani waited on the ball, and when he tried to clear, the ball struck Alfaro and sailed into the goal much to the joy of the home crowd.
Goa tried to fight their way back and carved two good chances towards the closing stages of the first half. In the 38th minute, Mandar Rao Desai got past two defenders on the left and pulled the ball back for Jofre Gonzalez whose shot was blocked by NorthEast goalkeeper Subrata Paul.
Just a minute before half-time, NorthEast survived again. This time it was from a Jofre free-kick which an unmarked Lucio squared it across the goal but before it reached the dangerous Rafael Coelho, the ball hit Robin Gurung and fell safely into the hands of the goalkeeper.
In the second session, Goa continued to attack and the NorthEast goalkeeper had to make a double save. Mandar was the first to test Paul from close range and then a long ranger from Trindade Goncalves was again parried away by the goalkeeper.
NorthEast increased their lead in the 63rd minute with some brilliant play. A through ball from just beyond the half-way mark was flicked into Alfaro's path by Holicharan Narzary and the Uruguayan striker did well to beat Kattimani from a narrow angle.
Alfaro should have scored his hat-trick in the 79th minute when he was within handshaking distance of the goal but his shot was saved on the line by Raju Gaekwad.
