Antwerp secured a second cup win in four years as they opened the scoring just past the half-hour mark when Mechelen defender Dries Wouters brought down Jurgen Ekkelenkamp in the box for a clear penalty.
Janssen had to re-take his spot-kick after he prematurely took the first effort before referee Jonathan Lardot had blown his whistle. The striker chose the opposite corner with his second attempt and netted again.
Mechelen were in the contest until the final 10 minutes when substitute Balikwisha, on the pitch for Janssen, scored Antwerp’s second goal following a quick counter-attack, converting a Calvin Stengs cross.
Antwerp will now enter the 2023-24 Europa League campaign in the final play-off round before the group stages.