Shikhar Dhawan, who was named the captain initially, will now be Rahul's deputy.
Rahul was recovering from a sports hernia surgery and was supposed to play the West Indies series before testing positive for COVID-19.
Since his recovery was taking time, he was not initially selected for the Zimbabwe tour and given time to get fully fit before the all-important Asia Cup.
However, the medical team has now given an all clear after he cleared all the requisite fitness parameters to be available for selection.
Since he is an all format first-choice deputy to regular skipper Rohit Sharma, his availability meant that Dhawan was relegated to vice-captaincy for the series.
Rahul's addition took the squad strength to 16 as the selectors didn't replace any player. But Rahul's presence means that there is virtually no chance for Ruturaj Gaikwad to get a game in this series.
There will be no Rohit Sharma, Virat Kohli, Rishabh Pant, Shreyas Iyer, Jasprit Bumrah or Mohammed Shami for this series as they had all been rested.
Bumrah, however, is nursing a back injury and is already ruled out of the Asia Cup in the UAE, starting August 27.
From this squad, Rahul, Deepak Hooda are the only two players in the main squad.
India Squad for 3 ODIs: KL Rahul (Captain) Shikhar Dhawan (vice-captain), Ruturaj Gaikwad, Shubman Gill, Deepak Hooda, Rahul Tripathi, Ishan Kishan (wicket-keeper), Sanju Samson (wicket-keeper), Washington Sundar, Shardul Thakur, Kuldeep Yadav, Axar Patel, Avesh Khan, Prasidh Krishna, Mohd Siraj, Deepak Chahar.