Matthaus, appointed last week, had named Bojinov in an 18-man squad containing only overseas-based players last week but left him out of his final squad after watching the striker in action against Fiorentina in Serie A on Sunday.
However, the Parma striker said he had not been dropped.
"From now on I'll decide whether to accept to play for the national team or not to play," Bojinov told Darik radio. "It's not Matthaus who decided to drop me from the squad. There are other things involved... but I can't tell the media now."
Bojinov's absence took fans and media by surprise as he was expected to start following Manchester United striker Dimitar Berbatov's decision to remain in international retirement despite Matthaeus's attempts for him to change his mind.
German Matthaus dropped Alania Vladikavkaz's attacking midfielder Ivan Stoyanov from his initial list.
The former World Cup-winning Germany captain surprisingly added eight home-based players to the squad with three of them debutants.
Uncapped Lokomotiv Sofia keeper Boyan Peykov, Litex Lovech defender Nikolay Bodurov and Cherno More Varna midfielder Daniel Dimov completed the 24-man squad for the Cardiff trip.
Matthaus, 49, has an uphill task to qualify the Balkan country for the Euro 2012 finals following back-to-back Group G defeats against England and Montenegro in the opening two qualifiers.
Four days after the Wales qualifier, Bulgaria meet Saudi Arabia in an international friendly in Istanbul.
