SAFFC went into Friday evening's game as favourites and were looking to make amends for last season's third-place finish, while there were question marks over the threat Albirex would pose after losing a number of key players over pre-season.
However, the White Swans drew first blood in the 26th minute when midfielder Musashi Okuyama found the back of the net, before striker Toshikazu Soya added a second just before halftime.
The game then looked all but over when Soya grabbed his second on the hour mark to put Albirex 3-0 up, but the Warriors were given a glimmer of hope when Croatian hitman Mislav Karoglan pulled one back from the spot.
Nonetheless, the Albirex defence stood firm to hold on to all three points, although they had to survive a late scare when Shukor Zailan added a second for SAFFC at the death with a screamer.
Last season's runners-up Home United looked uncharateristically toothless up front in Friday's other game, as they were held to a 0-0 draw by minnows Balestier Khalsa.
With star striker Frederic Mendy and new signing Shotaro Ihata - who scored more than 40 goals between them last season - leading the line, the Protectors were expected to put Balestier to the sword.
However, Lee Lim-saeng's men struggled to break down the visitors' defence for the most part, and ultimately had to settle for a point.
On Thursday, league newcomers Harimau Muda recorded an impressive 2-0 win over Gombak United with goals coming from Thamil Arasu and Wan Zaharulnizam , while Hougang United and Tanjong Pagar United played out a 1-1 draw.
Canadian striker Jordan Webb gave Hougang the lead in the 23rd minute, but Takaya Kawanabe equalised eight minutes later to earn the Jaguars a share of the spoils.
Sunday's action will see returning Bruneian outfit DPMM FC entertain defending champions Tampines Rovers, while Courts Young Lions face off against Woodlands Wellington.
Friday's S.League Results
Albirex Niigata 3-2 SAFFC
Home United 0-0 Balestier Khalsa
Thursday's S.League Results
Sunday's S.League Fixtures
DPMM FC vs Tampines Rovers
Courts Young Lions vs Woodlands Wellington