Delhi said Rabada had been advised to return by Cricket South Africa as a precautionary measure.
"It's hard for me to leave the Delhi Capitals at this stage of the tournament. But with the World Cup just a month away, a collective decision has been made for me in this regard," Rabada said in a statement.
Third-placed Delhi have qualified for the IPL playoffs and play Rajasthan Royals in their last league game on Saturday.
"It's been a tremendous season for me with Delhi Capitals, both on and off the field, and I truly believe that our team can win the trophy," Rabada added.
Rabada's fellow paceman Dale Steyn was also ruled out of the IPL last month after a flare-up of an old shoulder injury, putting his World Cup prospects in doubt.
South Africa open their World Cup campaign against England at The Oval on May 30.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Peter Rutherford)
