Austine Ogunye, Sikiru Olatunbosun and Stephen Odey scored for the Olukoya Boys, who now have 33 points.
Plateau United who did not play, are second with 32 points with one outstanding match.
El-Kanemi remain on 30 points and third on the log.
In Katsina, Enyimba threw away their one-goal lead to lost 2-1 to hosts Katsina United. Shooting Stars beat Niger Tornadoes 2-1 at the Lekan Salami Stadium, while Kano Pillars suffered their first home defeat of the season, losing 1-0 to Akwa United.
The home supporters resorted to violence after the match, invading the pitch and chasing the match officials off with dangerous objects.
Akwa United players and officials had to hide in the dressing room under heavy police protection.
In other fixtures, ABS beat Nasarawa 1-0 at home, Lobi were held to a 0-0 draw at home by IfeanyiUbah, Gombe lost 3-1 away to Wikki Tourist, Rivers United defeated Abia Warriors 1-0 and Sunshine edged Remo Stars 1-0 in Akure.