The 43-year-old from South Lanarkshire gave birth on Tuesday at a maternity unit in Greater Glasgow.
In a statement, she paid tribute to NHS staff who treated her in 2014 and those on the maternity ward who helped deliver her sons.
Cafferkey said: “I would like to thank all the wonderful NHS staff who have helped me since I became ill in 2014 right through to having my babies this week.
“This shows that there is life after Ebola and there is a future for those who have encountered this disease.”
A spokeswoman for NHS Greater Glasgow and Clyde said the mother and babies were “doing well”.
Cafferkey contracted Ebola while undertaking aid work in Sierra Leone during the West African Ebola epidemic. She spent almost a month in an isolation unit after being flown home.
The nurse survived the illness and was discharged from hospital, but has been readmitted on numerous occasions.
More than 11,000 people died in West Africa between 2013 and 2016, with a handful of cases treated in the UK. The outbreak was thought to have started in Guinea.