Morkel was a member of the party which played Australia in a one-day international series in April.
"South African cricket is blessed with an abundance of fast-bowling talent with the emergence of (Lonwabo) Tsotsobe and Wayne Parnell as outstanding new prospects and Charl Langeveldt becoming available again," said convenor of selectors Mike Procter in a statement.
"Langeveldt is not fit enough yet to be considered after his shoulder surgery and Morne Morkel is the unlucky one to miss out. He (Morkel) is very much part of our long-term planning and has a major role to play but we would like to see more consistency from him."
The 24-year-old Morkel has played in 21 ODIs, taking 31 wickets at an average of 30.16.
Left-arm swing bowler Tsotsobe, who has recovered from a long-term injury, and left-arm spinner Robin Peterson are the only new players in the squad.
"Planning for the 2011 World Cup is very much part of our thinking but there is a lot of cricket to be played before then," said Procter. "We must take our selections series by series and not get ahead of ourselves.
"We have four quality spin bowlers and two all-rounders in Jacques Kallis and Albie Morkel to back up the seam attack. There is also batting potential most of the way down the order."
The Champions Trophy takes place in South Africa from Sept. 22 to Oct. 5.
Squad - Graeme Smith (captain), Johan Botha, Hashim Amla, Mark Boucher, AB de Villiers, JP Duminy, Herschelle Gibbs, Jacques Kallis, Albie Morkel, Makhaya Ntini, Wayne Parnell, Robin Peterson, Dale Steyn, Lonwabo Tsotsobe, Roelof van der Merwe.
