The best chance of the half for Singapore came in the 15th minute, but Hami Syahin’s shot fizzed wide.
Joao Pedro continued to be a thorn in Singapore’s side as he almost pounced on another loose pass, but could not take the ball past an onrushing Izwan.
Singapore had the ball in the back of the net early in the second half courtesy of Lion City Sailors’ Abdul Rasaq. But the youngster had strayed offside after good work from substitute Safuwan Baharudin to hook a ball back in after a corner.
The Lions were unlucky not to have been awarded a penalty minutes later when Farhan Zulkifli was felled in the box by a defender, but one would soon arrive as Shawal was pushed by a defender while attempting to connect with a cross.
And Kyoga notched his first goal for Singapore as the newly naturalised Lion sent the Timor-Leste goalkeeper the wrong way from the spot.
There was confusion after as a Safuwan cross was tucked home by fellow substitute Shawal. While the 83rd-minute goal appeared to have been chalked off by VAR, it was eventually given.
Shawal would then wrap things up in the 90th minute with another close range finish.
Singapore will next face Thailand on Tuesday and then travel to Kuala Lumpur on Friday to face Malaysia.
The Lions had begun their campaign on Wednesday with a 2-1 win over Cambodia at the National Stadium.
A pair of first-half goals from Faris Ramli and Shawal Anuar gave Singapore three points against the plucky away side, who had outplayed the Lions for most of the game.
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