Shakir Hamzah had initially given the home side the lead from a similar set-piece just before half-time, as the LionsXII looked to capitalise on their home advantage at a fortress where they have been unbeaten for the last 18 months.
Although Fitri Shazwan struck back for the Red Giants in the 58th minute to draw them level, Amri broke the hearts of the visitors and their travelling fans by converting a bullet header in the last minute of additional time.
The LionsXII earned a 2-1 win over Selangor FA in an exciting encounter at the Jalan Besar Stadium on Saturday night, thanks to Khairul Amri's header in the dying seconds.
Selangor initially had the better start, with Shakir earning a caution as early as the third minute after failing to stop Juninho from marauding into the box. Dangerman Paulo Rangel then fluffed his shot wide from outside the box, with goalkeeper Izwan Mahbud looking stranded.
However, the LionsXII soon grew into the match and created chances of their own.
Amri arguably should have done better after latching onto a long ball in the box, but failed to get his shot on target.
Midfielder Hafiz Sujad was the next to come close in the 42nd minute after beating his marker and curling a strong shot in, but the Singapore international was unlucky to see the ball come off the bar.
But Shakir soon gave the LionsXII a deserved lead, capitalising on Selangor custodian Farizal Marlias’ missed interception from Zulfahmi Arifin’s corner to nudge the ball in superbly at the far post.
After the restart, Selangor came out more determined and soon grabbed an equaliser through Fitri. Juninho's out-swinging corner was met by Fitri, the shortest player on the pitch, who headed the ball beautifully past Izwan to tie the game.
The game was then littered with weak shots as both sides tried to force a winner, but the respective goalkeepers showed composure when called upon.
Just when the game seemed set to be heading for a stalemate, the LionsXII scored in the last minute of the game.
Substitute Shahfiq Ghani swung in a good corner from the left and Amri rose superbly to meet it with a thumping header to raise the roof of the stadium and hand the LionsXII their first points of the new season.