Pillars were forced to a 1-1 draw at home by Niger Tornadoes on Sunday.
They will finish in the top-10 bracket, which is widely regarded as a failure for a club who pride themselves of having won the Nigerian champions four times.
Babaganaru, who won the Pillars back-to-back champions three seasons ago, was posting his second spell at the club after he moved to Nasarawa United.
