Dhoni has been India's top performer in the series, which the hosts have already lost after going 0-2 down.
The Indian captain scored 113 not out in a losing cause in the first ODI in Chennai, while in Kolkata he was again the top scorer hitting an unbeaten 54.
"I am doubtful for tomorrow as of now. I suffered a back problem during the practice today," Dhoni told reporters on the eve of the game.
"Dinesh Karthik has been called up as my backup and we will take a final call before the match."
Speaking about Sunday's dead rubber, Dhoni said: "It's important for us to prepare for the next series. We will feature our best eleven for the match."
Dhoni though backed under fire coach Duncan Fletcher, saying that coaches only had a limited role and it was up to to the players to perform on the field.
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"Players need to take responsibility. Coaches can only do so much, it is the players who would finally have to perform on the field. The utmost responsibility lies with an individual," he said.
He rued the fact that the Indian team had failed to put pressure on the visiting Pakistan team and said that the entire team as a unit had failed to fire.
"This series we haven't batted well. In the earlier series sometimes our batsmen would do well and sometimes our bowlers. As a combined unit we have failed to perform."
Dhoni shrugged off questions on the growing pressure over his status as the captain of team.
"If I started taking pressure after every match and listened to everything the media and the others had to say, I would have crumbled by now," he commented.
"Everyone has a right to their opinions and we respect that but in the end we have to make the final call keeping the interests of the team in mind."