Abbott was ruled out for up to four weeks due to a side strain suffered in the ongoing Big Bash League and will miss the three-match series from January 14-19.
"It is extremely unfortunate for Sean who is very much a part of our white-ball squad plans leading into the ICC T20 World Cup and the World Cup," selector Trevor Hohns was quoted as saying by www.cricket.com.au.
"D'Arcy offers the squad another spinning all-rounder option along with Ashton Agar, which along with the four world class fast bowlers and Adam Zampa balances the squad out nicely. His proven record and ability to bat anywhere in the order will also be a great asset to the squad."
Australia already have pacers Pat Cummins, Josh Hazlewood, Mitchell Starc and Kane Richardson to bolster to their arsenal against the Men in Blue.
Australia ODI squad: Aaron Finch (c), Ashton Agar, Alex Carey (vc), Pat Cummins (vc), Peter Handscomb, Josh Hazlewood, Marnus Labuschagne, Kane Richardson, D'Arcy Short, Steve Smith, Mitchell Starc, Ashton Turner, David Warner, Adam Zampa