Mu Kanazaki marked his first appearance for the Samurai Blue in five years with his first goal for his country in the 20th minute with Keisuke Honda and Maya Yoshida also notching in a lop-sided contest at the National Stadium.
The victory moved Japan top of Group E with 13 points from five matches, with Singapore in third on 10 points ahead of next week's crunch match at home to Syria (12 points) in the battle for second place in the five-team pool.
The eight group winners and four best runners-up will qualify for the 2019 Asian Cup and also advance to the third round of a lengthy World Cup qualifying campaign in Asia which will eventually provide four teams for Russia 2018.
Japan's only slip up in qualifying so far was a 0-0 goalless draw at home to 152nd FIFA ranked Singapore in June and head coach Vahid Halihodzic said his side were out for revenge in Thursday's return.
The coach left Shinji Kagawa and Shinji Okazaki on the bench but the absence of the two-European based players mattered little as Japan were quick into gear against hospitable hosts, who retreated and struggled to contain possession.
Singapore goalkeeper Izwan Mahbud had already made a number of smart stops before Kanazaki produced a brilliant finish to open the scoring.
Honda lobbing the ball into the area which Yoshinori Muto nodded down and the Kashima Antlers attacker, who is on loan from Portuguese side Portimonense, controlled on his chest before firing an unstoppable left foot effort past Izwan.
The goal rattled the hosts and they were quickly two behind. The Singapore backline failed to clear a ball into the area and Honda's deflected shot went cruelly out of Izwan's reach in the 26th minute.
Japan toyed with their opponents from then on with Izwan kept busy as the visitors easily created chances.
Their intensity did drop in the second period, though, and Singapore midfielder Muhammad Safuwan came close to pulling a goal back just after the hour mark but his header dropped just wide of the far post.
Halihodzic brought on the talented Takashi Usami and Kagawa for the final quarter of the game but it was central defender Yoshida who grabbed the third as he deflected Usami's strike home in the 87th minute.
Japan travel to Cambodia for another qualifier on Tuesday.
(Editing by Pritha Sarkar)
