In the end, goals from Matthew Kelvin Andoh and Emmanuel Gyamfi proved decisive in the preliminary round fixture at Kumasi's Baba Yara Stadium.
“This [qualification] is what we have always wanted," Annan said after the game, as reported by Footballghana.
"We got the experience [of playing in Africa] from last season and it was something special. So for us to qualify to the next round is really exciting for us.
“We are really happy that we are going to the next round because it would have been a big blow if we couldn’t qualify.
"The expectation was really high and looking at the fans, if you don’t win for them, you as a footballer it feels your job hasn’t been done."
Kotoko are set to face Etoile Sahel of Tunisia in the next round.
The Porcupines, who reached the Group Stage of the Caf Confederation Cup last season, have set a target making it to the 'money zone' of the Champions League this season.
Their last appearance in the elite continental inter-club championship ended in a first-round exit.