The two African stars were on target for their teams on Tuesday night but the Serbian champions progressed after the game went into penalty shoot-out
Following a 1-1 draw in the first leg of the fixture, Boakye opened the scoring at the Telia Parken to put the visitors ahead in the 17th minute.
However, the lead was short-lived as Ndoye ensured both teams head into the interval levelled with his 44th-minute equaliser for Copenhagen.
After the restart of the game, the two teams struggled to score a winner and then proceeded to penalty shoot-out following a 2-2 aggregate score at the end of 120 minutes.
Article continues below
— F.C. København (@FCKobenhavn) August 13, 2019
Boakye was missing in the shoot-out because he was replaced in the 81st minute while Ndoye failed to convert his chance from the penalty spot.
Red Star Belgrade advanced to the next qualifying round of the elite European competition with a 7-6 win on penalties.
They will meet Swiss Super League outfit Young Boys next Wednesday for the first leg of the Champions League playoff.