Former skipper Terry retired ahead of the FA hearing which banned him for four games and fined him £220,000 for racially abusing Anton Ferdinand.
Striker Rooney, 26, said: “John has been fantastic for us, he’s an old-fashioned centre-half, not afraid to get his foot in. He has been great.
“Obviously he has made his decision to retire and we have to respect it.
“But of course he will be a loss to us. Him and Paolo Maldini are probably the two toughest defenders I have played against.”