All-rounder Flintoff was initially named in the 15-man Champions Trophy squad but was subsequently ruled out of the tournament after having surgery on a knee injury.
The Champions Trophy event technical committee has approved the replacement of Flintoff with Onions for the tournament in South Africa from Sept. 22 to Oct. 5.
Fast-medium bowler Onions has been in previous England one-day squads but has not played an international.
He made his England test debut this year against West Indies and featured in the Ashes series victory over Australia.
He will join the England squad on Tuesday as the team prepares for the third one-dayer against Australia in Southampton on Wednesday.
Australia lead the seven-match series 2-0.
Squad: Andrew Strauss (captain), James Anderson, Ravi
Bopara, Tim Bresnan, Stuart Broad, Paul Collingwood, Joe Denly, Eoin Morgan, Graham Onions, Matt Prior, Adil Rashid, Owais Shah,
Ryan Sidebottom, Graeme Swann, Luke Wright.
Pietersen in England's Champions Trophy squad
Flintoff withdrawn from Champions Trophy squad
Yorkshire pacer Bresnan in England Test squad
England stars to miss Champions League
England leave out Vaughan, Harmison