The Irishman is expected to be out of action for six weeks after having an operation to tidy up a cartilage problem on Tuesday.
The 31-year-old was the club's top goalscorer last season but faces added competition from summer signings Kris Boyd and Kenny Miller and will have to watch from the sidelines from the start of the campaign.
Rangers manager Ally McCoist told the club website: "It's a real shame. Big Jon was fantastic for us last year as he scored 25 goals.
"Towards the end of the season, we would have given him a little rest if we could have but personnel indicated we couldn't.
"With Andy Little injured, he was our only striker at points and, to be fair to him, he kept turning up and playing for us.
"He was playing through a little bit of pain then had a good rest in the close season but there is still a little niggle there.
"We sent Jon for a scan and that showed he has a problem with his cartilage so he has gone back to the same surgeon who did his other knee.
"It looks as though he will be out for six weeks and it's a blow for the team. It's obviously blow for him too but the bottom line is he has to get it sorted as quickly as possible.
"Our doctor has spoken at great length with the surgeon and he's very confident he'll get it cleaned up."