Kallis is being rested ahead of the ICC World Twenty20 in September. Imran Tahir has been included as a specialist spinner while Ryan McLaren has been recalled as an additional seamer.
"Dean has been in our plans for some time and might well have made his debut last year but for injury, while Imran is a genuine wicket-taking bowler and his selection enables us to explore our options in this area," said Cricket South Africa selection convener Andrew Hudson.
"Ryan has just come off some exceptional form for the South Africa A side and the added depth he provides in the seam bowling department will allow us to rotate players if we feel the need arises."
Five members of the Proteas' squad -- Wayne Parnell, Faf du Plessis, Justin Ontong, Elgar and McLaren -- will travel to Ireland for the South Africa A side's first ODI there and then join the rest of the squad in England.
The squad:
AB de Villiers (capt), Hashim Amla (vice-capt), JP Duminy, Faf du Plessis, Dean Elgar, Imran Tahir, Ryan McLaren, Albie Morkel, Morne Morkel, Justin Ontong, Wayne Parnell, Robin Peterson, Graeme Smith, Dale Steyn, Lonwabo Tsotsobe.