The Italian forward was heavily criticised for his performance in the Reds' 3-0 loss to Madrid at Anfield in their Group B encounter.
The 24-year-old has also sparked controversy for swapping shirts with Madrid defender Pepe during the half-time interval.
While Owen has admitted that he is not Balotelli's biggest fan, the former Liverpool and Manchester United striker believes that the Italian does not deserve to be singled out.
"I'd still start Balotelli at the weekend," Owen wrote on Twitter. "I'm not a big fan of his but he has more class than most. Harsh to put all the blame on him.
"Last point on Balotelli. Most worrying thing is his teammates' body language towards him. Once you lose their respect it's a big struggle."
Balotelli has scored just once for Liverpool following his move to Merseyside from AC Milan in the summer.