The ex-England Under-21 international had been hospitalised since suffering a fall at a pub in Barry on March 7.
It was revealed by South Wales Police that Whittingham had suffered head injuries and was in a serious condition.
A statement read: “At around 10pm on March 7, South Wales Police were called to a licensed premises in Barry.
“A 35-year-old man from Penarth suffered a head injury as a result of a fall and remains at the University Hospital of Wales, Cardiff.
“At this stage there is no evidence or suggestion of a criminal act, and it appears the injury was caused by an accidental fall.
“Enquiries are continuing into the circumstances of the incident.”
It has now been confirmed that Whittingham lost his fight for life on Thursday morning.
His former employers at Cardiff have led the tributes to a man who spent 10 years on their books, taking in 459 appearances and scoring 98 goals.