Non-striker David Hussey answered his partner's call but as he was completing the run, the Aussie put his right hand out to stop the ball from hitting him.
Indian skipper Dhoni appealed for an obstructing the field dismissal which is allowed under the ICC rules.
Bowden and Taufel referred the matter to third umpire Simon Fry, who decided in favour of the batsman by concluding that he was merely trying to avoid getting hit himself instead of saving the stumps.
Dhoni was not quite happy with the decision and had a chat with Bowden about it for quite some while.
In Image: India's Virat Kohli, left, has words with Australia's David Hussey after he lost his wicket for 54 runs