Pant suffered a blow to the helmet from a rising Pat Cummins delivery, which resulted in his dismissal.
He was unable to connect his bat to the steep short ball that caught the outside edge of the blade before striking him flush on the helmet and was caught by the fielder stationed at point.
He could not fulfill his wicketkeeping duties in Australia's run-chase with KL Rahul stepping up to perform glovework responsibilities.
Pant will now undergo his rehabilitation protocol according to the standard ICC procedures in place.
While the rest of the India squad will make their way to Rajkot, the dynamic southpaw will be travelling to the National Cricket Academy in Bengaluru.
"He [Pant] is ruled out of the 2nd ODI. His availability for the final ODI will be based on how he responds during the rehabilitation protocol," BCCI said in its statement.
Amidst fears regarding Pant's safety, the youngster has been declared stable and was duly discharged from the hospital.
"He is stable and all his scan reports are clear. He has been discharged from the hospital and will head to NCA, Bengaluru to undergo his rehabilitation protocol," the press release further stated.
Pant's absence opens the doors for either Manish Pandey or Kedar Jadhav's inclusion in the playing XI for the second ODI clash if the team management opts to strengthen the batting department.
On the other hand, India could go for seam-bowling all-rounder Shivam Dube to bolster their bowling resources following the 10-wicket hammering by Australia.
With a possibility of Pant recuperating from concussion for the final ODI at the M. Chinnaswamy Stadium, India have not yet named a replacement for the 22-year-old.