For the second week in a row, centre-back Kunihiro Yamashita found the back of the net for the White Swans when he scored in the 56th minute, repeating his feat in last Friday's 2-1 loss to Balestier Khalsa.
However, the Jaguars looked to have grabbed a share of the spoils after Jordan Webb equalised from the penalty spot in the first minute of injury time, only to see Albirex captain Norihiro Kawakami grab a sensational winner three minutes later following Takeshi Ito's cross.
The White Swans triumph at the Hougang Stadium was their first since a 1-0 win over Woodlands Wellington at the Jalan Besar Stadium on March 1, and ends a wretched run of form which saw them pick up just one point from their last four matches.
"All the players, all the staff and all the supporters never gave up and that's why we won," declared Albirex's jubilant coach Koichi Sugiyama.
"It was unfortunate that we conceded a goal so late, but we were never worried becuase we comtrolled almost the whole game," he added.
It was an equally dramatic evening over at the Hassanal Bolkiah National Stadium as DPMM FC reclaimed top spot with a 3-2 win over Tanjong Pagar United.
The Bruneian outfit looked headed for a comfortable outing after Shahrazen Said's first-half brace put them 2-0 up at the break.
And the game looked all but won nine minutes into the second half when Subhi Abdilah grabbed a third, only for Takaya Kawanabe to pull one back from the spot in the 66th minute.
Three minutes later, Asraf Rashid grabbed a second for the Jaguars to ensure the closing stages would be a nervy one for DPMM, although they eventually held on to all three points to leapfrog Balestier back into top spot.
On Thursday, Balestier recorded an impressive 1-0 win over SAFFC courtesy of substitute Andrew Tan's 69th-minute winner, while goals from Michael King and Jozef Kaplan helped Geylang United to a 2-0 victory over Courts Young Lions.
Friday's S.League Results
Hougang United 1-2 Albirex Niigata
DPMM FC 3-2 Tanjong Pagar United
Thursday's S.League Results