Rodgers himself is also coming under scrutiny, with Liverpool struggling in the Champions League and sluggish in the Premier League since the sale of star striker Luis Suarez to Barcelona.
At 3-0 down at half-time on Wednesday, Balotelli had shown none of the bite or brilliance that took him to Inter Milan, Manchester City and AC Milan, and Rodgers says he would have been subbed even without the shirt swap with Pepe.
“I only heard about it when I came off the pitch (after the game),” he said.
“For me, if you want to do that it’s something you do at the end of the game. I will deal with that tomorrow (Thursday).”
The highly-rated but unpredictable Balotelli has scored just once in 10 appearances for Liverpool, and Rogers had lost patience with a lack of endeavour from the giant striker.
Former Liverpool captain Graeme Souness was equally scathing of the Italian’s performance against Madrid.
“You never watch Mario Balotelli and think ‘Wow, he’s put a real stint in’.
“The criticism is for him not showing any enthusiasm,” said Souness.
But the former Scotland international also pointed the finger at Rodgers for signing Balotelli in the first place after other top managers had failed to get a decent return from the eccentric Italian.
“Roberto Mancini twice, Jose Mourinho had one look at him and very quickly said ‘I can’t work with this guy’, Cesare Prandelli said after the World Cup he made a giant mistake taking him to Brazil,” he explained.
“What makes you (Rodgers) think you can get something different from him?”
Against Madrid Rodgers got little indeed from Balotelli, but praised another of his summer signings, the man he brought on at half-time Adam Lallana.
“In the second half you could see every player pressing and working,” insisted Rogers.
“At Liverpool that is the minimum we expect. You could see Adam Lallana when he came on he was tireless in his work.”
Ahead of a fear-inspiring trip to Madrid, the Reds now lie third in Champions League Group B with defeats to both Basel and Madrid and their single win coming against Bulgarians Ludogorets.
They are, however, fifth in the Premier League, albeit nine points adrift of leaders Chelsea.
Ballotelli and Rodgers under Anfield spotlight