The Italy international, who has scored just once in 10 games for the Reds since joining from AC Milan in the summer, was caught making the exchange with Pepe in the tunnel area at Anfield
Balotelli did not emerge after the interval, although Rodgers quickly brushed it aside as being nothing more than a tactical change.
However, when asked for his views on the shirt-swapping incident, the Northern Irishman told Sky Sports News: "That's the first I've heard about it and I wouldn't like it. It's something that doesn't happen here, it shouldn't happen here.
"We had a case of a player doing that last season, which I dealt with, and if that's the case again then I'll deal with it again."
The defeat leaves Liverpool in third place in Group B, level on points with Ludogorets Razgrad who occupy the second qualifying berth.