In Friday's other game, Brunei's DPMM FC handed Geyland United their fourth successive defeat of the season to leave V. Kanakarajan's side rooted to the bottom of the table.
At the Choa Chu Kang stadium, SAFFC stormed into a three goal lead in the first-half - thanks to strikes from Mislav Karoglan, Seiji Sato and Shimpei Sakurada.
However, Robin Chitrakar's boys showed good fighting qualities to reduce the deficit to two goals before the interval when Jonathan Toto bundled the ball past SAFFC keeper Hassan Sunny.
The home side restored their three-goal advantage thanks to a bullet header from Fazrul Nawaz soon after the break, but Young Lions ensured a nervy finish with Toto grabbing his second and Benjamin Lee getting the side's third with a little over 10 minutes remaining.
There were to be no more breakthroughs though, as SAFFC held out to stay at tenth in the table and move to within a point of ninth-placed Gombak United.
Over in Brunei, Geyland United's miserable start to the season continued as they were thrashed 4-1 to ensure their hunt for that elusive first point goes on.
Goals from Shahrazen Said and Basiru Osman gave DPMM a two-goal lead just after the half hour mark, but when Jozef Kaplan's penalty reduced the margin to one, there seemed to be hope for the visitors.
It proved to be a false dawn, as Tales dos Santos and substitute Helmi Zambin put the game beyond Geylang's reach with a goal apiece in the second half.
The result propelled DPMM to the top of the table with three wins and a draw from their four games.
Geylang meanwhile were left wondering where their first point is going to come from.