The incident happened in the 63rd over of India Blue's second innings as Ojha, while fielding for India Green at mid-on, was dealt a blow on the left side of his head after the ball bounced viciously in front of him, forcing him to take evasive action.
The ball came from the bat of Pankaj Singh and Shreyas Gopal was the bowler.
The impact brought him down immediately and he was stretchered off the ground.
Later, he was taken to the nearby hospital for tests including a CT scan.
"Pragyan Ojha suffers freak head injury in @Paytm Duleep Trophy match, taken to hospital for tests," the BCCI tweeted on the incident.
However, BCCI later posted that Ojha was fine along with his cheerful picture taken in the hospital.
"Pragyan Ojha is doing fine. His health will be monitored," wrote the BCCI in its subsequent tweet.
Ojha went wicket-less in the first innings before taking three in the second essay of India Blue which ended at 288 in 66.2 overs, setting the Green team an improbable 769-run target on fourth and final day of the game.
India Blue had posted a mammoth 707 in the first innings and India Green in response could only manage 237.