Forced to miss out on a host of first choice players against a much superior team, the Indians gave a good account of themselves during Saturday's match.
Jordan captain and goalkeeper Amer Shafi Mahmoud Sabbah scored his first international goal with a long clearance to give his team the lead in the 25th minute.
Ihsan Haddad doubled the lead with a well placed finish in the 58th minute after the hosts caught the Indian defence off guard with a fast counterattack down the left.
An unmarked Nishu Kumar pulled one back for India in the 61st minute when Germanpreet Singh made a run into the Jordan penalty box and found him with an accurate pass which caught the defenders napping.
The visitors were forced to leave a host of first choice players -- including almost their entire forward line -- on the bench after their travel plans went awry due to heavy rains in Kuwait.
While Sunil Chhetri was yet to recover from an injury, Sandesh Jhingan, Narayan Das, Udanta Singh, Halicharan Narzary and Jeje Lalpekhlua were also missing.
They were replaced by Anas Edathodika, Salam Ranjan Singh, Germanpreet Singh, Vinit Rai, Jackichand Singh and Jerry Lalrinzuala.Also Read: Barcelona star Ivan Rakitic out for three weeks with hamstring strain
Forced to field a team packed with defenders and midfielders, the Indians were extremely well organised in defence and frustrated the Jordanian forwards for the better part of the game.
The hosts on the other hand, were more composed on the ball. They tried to hold possession and create moves from the back with short passes.
The referee came up with a controversial decision when he awarded an inexplicable penalty to Jordan in the eighth minute after Al Ersan slammed in an at tempted low cross which hit Pritam Kotal on the arm from close range.
But Indian goalkeeper Gurpreet Sandhu dived the right way to produce an excellent save and keep out Bani Attiah's attempt to the lower left corner.
Gurpreet however produced a blunder to concede a soft goal and virtually gift the lead to Jordan.
Amer had sent a long clearance into the Indian box and Gurpreet, who was off his line, misjudged an awkward high bounce only to see the ball nestle into the back of the net.
Baha Faisal missed a sitter a couple of minutes before halftime when a rare mistake by the Indian defence saw him at the receiving end of a Hadad pass in side the six-yard box with only an off-guard Gurpreet to beat.
But Faisal fluffed what should have been a simple tap in.
The hosts doubled their advantage shortly after the break when the Indians lost the ball in the Jordanian half after a corner. The visitors had committed too many players near the Jordanian box most of whom failed to fall back as the hosts launched a quick counterattack.
Ahmed Samir laid a well placed pass from the left for Hadad, who had made an excellent run from the defence.
With no defenders marking him, Hadad bulged bulged the net with a powerful, accurate finish from near the edge of the penalty box.
Nishu reduced the margin only two minutes after coming on a substitute for Jackichand.
But the visitors did not have the quality to create a second goal as Jordan claimed a well deserved victory.