Frankfurt's plans for next season were thrown into chaos on Friday when Bundesliga champions Bayern confirmed Kovac, 46, will join them to replace Jupp Heynckes as coach in 2018/19.
"Trainers and players come and go, my team will not use this as an excuse," Frankfurt coach Kovac told 'Sky'.
"Everyone is professional enough, because we know we can achieve a European place next year - I am convinced of that."
However, the performance at the BayArena did not back up Kovac's words as Frankfurt's Champions League hopes suffered a heavy blow, as they fell 4-1 to Leverkusen - the first time this season Frankfurt have conceded four goals.
Germany hopeful Kevin Volland boosted his chances of making Joachim Loew's World Cup squad, to be named on May 15, with a hat-trick for Leverkusen.
However, compatriot Julian Brandt gave Leverkusen the lead with a deft header -- his first in the Bundesliga -- on 20 minutes.
Frankfurt drew level just three minutes later when Mexico midfielder Marco Fabian rounded the goalkeeper to finish a move started by Kevin-Prince Boateng.
Then teenage winger Kai Havertz threaded a pass through the Frankfurt defence to Volland, who tucked his shot into the bottom corner on 71 minutes to make it 2-1. The floodgates opened soon after.
Volland's second goal came six minutes later when Brandt broke through the middle and played Karim Bellarabi in behind the defence.
The winger handed Volland a simple tap-in, and the striker then claimed his 14th goal of the season to wrap up his hat-trick.
Bellarabi beat the defence and again served up another a goal for Volland two minutes before the final whistle.
The win cements Leverkusen's grip on fourth place and gives them a five-point cushion over Hoffenheim, in fifth, and Frankfurt, who are in the Europa League places.
14 April 2018