The former Doctor Feelgood star underwent complex surgery to remove a large tumour and extensive sections of his digestive system.
The 66-year-old had previously chosen to avoid treatment after being told he had terminal pancreatic cancer in late 2012.
But recent tests showed it was not as aggressive as had been previously thought, and the operation was offered as a chance to save his life.
Johnson has cancelled a string of commitments including an appearance at the Glastonbury festival to allow himself time to recover.
His manager, Lisa Climie, said: "The head of the medical team treating Wilko said that they were happy with his condition. Wilko will stay under very close observation for the next few days.
"Although cautiously optimistic, the team have to stress that it is very early days yet."
Johnson enjoyed his biggest success for decades earlier this year thanks to his Going Back Home album with The Who's Roger Daltrey.
The musician, who has also appeared in TV hit Game Of Thrones, underwent the operation at Addenbrooke's Hospital in Cambridge.