At 119 for four, Australia were rather precariously poised when wicketkeeper-batsman Matthew Wade took off for a single off R Ashwin's final delivery of the over.
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 allowed under the ICC rules.
On-field umpires Billy Bowden and Simon 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 an animated chat with the umpires for quite some while.
India was earlier at the centre of another run out drama in a previous match when Sri Lankan Lahiru Thirimanne's stumps were removed by Ashwin at the non-striker's end as the batsman had been backing up far too much despite repeated warnings.
In that instance, India's stand-in skipper Virender Sehwag had decided to withdraw the appeal as he felt it was against the spirit of the game.