The Ghanaian attacker scored with 17 minutes left but his consolation was not enough after the visitors netted twice in the first half.
CSKA Sofia opened the scoring after just three minutes through Henrique, before Georgi Yomov doubled the lead 33 minutes later.
A second half strong fight from Ludogorets only saw them pull one back.
Elvis Manu’s strike sees him reach double figures in his first season with the Bulgarian giants, having netted ten times in all competition.
His compatriot Bernard Tekpetey missed the game through suspension.
