Substitute Yasuhiro Yamakoshi capitalised on some indecisive defending to bag the only goal of the game in the second minute of injury time, condemning the brave Rams to their first defeat of the season.
Both sides came into the game with maximum points from their opening two games, and with the outright lead in the league up for grabs, there was certainly plenty to play for.
Albirex started the brighter of the two teams, looking sharp with some crisp passing in the middle of the park, and gave the hosts no time to settle on the ball with their constant pressure.
In particular, Sho Kamimura was looking dangerous down the left, and it was no surprise he carved out the first opening early on when he picked up the ball in his own half and headed straight for the Woodlands goal, although he failed to find Toshikazu Soya with his delivery.
Despite their opponents having the upper hand in the possession stakes, the Rams, to their credit, remained patient and disciplined, and almost took the lead in the 11th minute against the run of play.
Breaking on the counter-attack in a three-on-three situation, Moon Soon Ho held on to the ball for just long enough before sliding in Guntur Djafril, who pulled off a clever save from Takuma Ito with a snapshot.
Kamimura continued to provide an outlet for the White Swans down the left and went on another penetrating run minutes later, although he could not find a team-mate with his cross once again after easily gliding past Woodlands skipper Daniel Hammond.
Despite their dominance, Albirex were struggling to find a way past the hosts' stubborn backline, and the in-form Soya began to cut an increasingly frustrated figure up front. On the other hand, the Rams were content in making the most of whatever possession they had, with both Moon and Hussein Akil looking dangerous on the break.
Albirex began the second period the same way they started the first, and just two minutes after the restart, a brilliant over-the-top ball from captain Norihiro Kawakami found Hidekazu Yamamoto unmarked in the box. However, just as the right-back was about to pull the trigger, Duncan Elias put in a superb sliding challenge to make the block.
Despite the lack of supply, Soya remained enthusiastic up front; regularly making runs in behind the Woodlands defence, and it seemed only a matter of time before he got one right.
And that moment arrived in the 73rd minute when Musashi Okayama found him with a clever reverse pass, only for Hammond to deny the Albirex striker with a brilliant block.
At the other end, Akil was looking increasingly dangerous for Woodlands whenever they broke forward, and twice tested Ito in the Albirex goal with stinging drives from outside the box.
Fifteen minutes from time, Moon must have thought he had broken the deadlock when he struck a brilliant volleyed-lob from 25 yards, only to have the backpedalling Ito deny him with a desperate save.
Three minutes later, the game looked destined for a goalless stalemate when Albirex substitute Keita Kobayashi blasted over from six yards with the goal at his mercy, after left-back Takeshi Ito had broken through down the left and slid in the perfect pass.
Alas, just when Woodlands thought they had managed to hold on to a creditable point, Yamakoshi, who had come on for Soya, pounced on a mix-up between Fabien Lewis and Ahmadulhaq deep into injury time, nipping in ahead of the Rams duo to tap home into an unguarded net.
Woodlands Wellington: Ahmadulhaq Che Omar, K. Sathiaraj, Fabien Lewis, Daniel Hammond, Duncan Elias, Armanizam Dolah, Shamsurin Rahman, Goh Swee Swee, Guntur Djafril (Farizal Basri 82'), Hussein Akil, Moon Soon Ho.
Albirex Niigata: Takuma Ito, Hidekazu Yamamoto, Norihiro Kawakami, Kunihiro Yamashita, Takeshi Ito, Shuhei Hotta, Atsushi Shimono, Masatake Sato (Keita Kobayashi 66'), Sho Kamimura, Musashi Okuyama, Toshikazu Soya (Yasuhiro Yamakoshi 85').