Rahaggu Yusuf handed the Sai Masu Gida side an early lead, but the Ghanaians rallied to draw level and went ahead soon after.
However, the reigning cup holders came back on level terms before the halftime break.
Ageless Gambo Mohammed scored the decisive goal late on to ensure Pillars take a slim 3-2 advantage going into the return leg in Accra in a forth night.
In the CAF Confederation Cup, Niger Tornadoes failed to make their home advantage count as they lost 2-1 to visiting Santoba of Guinea at the Ahmadu Bello Stadium, Kaduna.
Completesports.com reports that Tornadoes will need all the guts and nuts to overturn the first leg deficit when they travel to Conakry, Guinea, for the reverse fixture.
On their part, Kano Pillars will need to avoid defeat in Accra in the second leg to seal a place in the next round.
Enyimba, on their part, will must win, with t least two-goal difference, in the return leg in Aba to go through.
Rangers, Nigeria’s second entrants in the Confederation Cup were drawn bye in the First Round games.
