Luis Pinheiro (26th minute), Umero Embalo (51st) and Matos (70th) hit the target for the hosts here on Friday night.
The match was part of the exposure trip to Europe for the Indian boys who will take part in the U-17 World Cup later this year.
The Indians had claimed a 2-2 draw against the same club on April 27.
The Indian boys started on a positive note and came very close to scoring in the first 15 minutes.
Sanjeev put in an accurate pass for Aniket but the striker narrowly missed the target.
Just before the half-hour mark, the hosts drew first blood from a well-taken corner. Luis Pinheiro collected the long ball and rattled the back of the net to put his team in the driver's seat.
For India, Amarjit played a long ball down the right flank but Komal, having received it, couldn't penetrate the gutsy Benfica defence line. On the rebound, Aniket tried his luck but the Benfica goalkeeper had no problem collecting the ball.
Five minutes before the break, Rahul dribbled past several Benfica defenders but his long-ranger sailed over the crossbar.
Benfica doubled the lead just six minutes into the second half when Umero Embalo's shot got a heavy deflection off Rahul and hit the back of the net.
Matos netted the third goal for the hosts in the 70th minute to add to the visitors' woes.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
About VDC
Doraiah Chowdary Vundavally is a Software engineer at VTech . He is the news editor of SocialNews.XYZ and Freelance writer-contributes Telugu and English Columns on Films, Politics, and Gossips. He is the primary contributor for South Cinema Section of SocialNews.XYZ. His mission is to help to develop SocialNews.XYZ into a News website that has no bias or judgement towards any.