Gambo Mohammed scored the winning goal for the Nigerian champions just past the hour mark.
Former Heartland man, Abdul Haruna, did all the work and squared for Gambo to tap the ball in from close range past Kazeem Yekeen in goal for Bayelsa United.
It was all Pillars in the opening 45 minutes as Gambo, Ezekiel Mbah, Adamu Hassan and Haruna all went close to scoring.
At a point Yekeen had to make a big save to deny Mbah from scoring.
But the champions also had to pay a bitter price for the win as centre-back, Umar Zango, left the pitch injured following an aerial challenge with West Sobomabo. He was replaced by former Nigeria junior international, Kingsley Udoh.
Gambo's fourth goal of the campaign proved enough to ensure Kano Pillars go top of the standings on 31 points, same as second-placed Nasarawa United who have an inferior goal difference.
In another match, Abia Warriors compounded the troubles of Nembe City by bashing them 4-0 at the Umuahia Township Stadium.
Peter Onyekachi scored a hat-trick while Jackson Daniel got among the goals to condemn City to bottom place.
Abia Warriors have now climbed to the third position following the victory on the eve of the Fifa World Cup finals. They are just a point behind the league leaders.