The 21-year-old Pant was the backup to former captain and regular stumper Mahendra Singh Dhoni during India's home five-match series against West Indies.
Pant played three of the five matches as a specialist batsman and scored 17 and 24 in the second and third ODIs. Karthik, 33, has played 86 ODIs and was part of India's Asia Cup squad but was left out for the West Indies matches.
"After returning from Australia post the test series, Rishabh Pant will play for India A in the five-match one-day series at home against England Lions," the Indian cricket board said in their statement while announcing the squad.
Karthik was inconsistent and could not convert starts into big scores at the Asia Cup and finished with a total of 146 in six matches, missing the opportunity to secure the number four spot India have been looking to fill ahead of the 50-over World Cup next year.
But Karthik could well have sealed the spot with captain Virat Kohli and coach Ravi Shastri confirming recently that India's period of experimenting with their ODI side is over with five months left before the World Cup in England.
After the conclusion of the ongoing four-test series against Australia, India will play a three-match one-day international series in January.
That will be followed by a five-match ODI series in New Zealand before India return home for another five-match ODI series against Australia.
India's top players will then be involved in the Indian Premier League Twenty20 tournament before the World Cup begins on May 30 in England.
Manish Pandey, who has also auditioned for the middle-order spots, was also axed from the ODI squad after warming the bench against West Indies.
With the return of frontline seamers Jasprit Bumrah and Bhuvneshwar Kumar, Umesh Yadav found himself out of favour. Mohammed Shami and Khaleel Ahmed were the other quicks in the squad while all-rounder Hardik Pandya also returned to the squad after recovering from injury.
India also named their squad for the three-match Twenty20 series in New Zealand which was highlighted by the return of Dhoni after the long-serving cricketer was left out of their shortest format matches against West Indies and Australia.
Squad: Virat Kohli (captain), Rohit Sharma, Lokesh Rahul, Shikhar Dhawan, Ambati Rayudu, Dinesh Karthik, Kedar Jadhav, MS Dhoni (wicketkeeper), Hardik Pandya, Kuldeep Yadav, Yuzvendra Chahal, Ravindra Jadeja, Bhuvneshwar Kumar, Jasprit Bumrah, Khaleel Ahmed, Mohammed Shami
(Reporting by Sudipto Ganguly; editing by Pritha Sarkar)
