The incident was captured during the Millers 2-0 win over their derby rivals on Saturday afternoon with the footage later emerging on Twitter.
The two men were mocking a Rotherham supporter by rocking backwards and forwards in what appeared to be an imitation of an autistic fan who was 'stimming' during the game.
Doncaster now believe they have found those responsible and plan to reach out to the Rotherham supporter and offer them a VIP experience when the sides meet later in the season.
Shaun Lockwood, chief operating officer at Club Doncaster, provided an update via Twitter: "Quick update re [sic] the video. Thanks to all who sent info, we believe we have identified the individuals. The club will act accordingly. We're also going to make contact with the Rotherham United supporter to offer them a VIP experience at the return fixture with Doncaster."
According to the National Autistic Society, stimming, or self-stimulating behaviour, includes arm or hand-flapping, finger-flicking, rocking, jumping, spinning or twirling, head-banging and complex body movements.
People with autism use self-stimulating behaviour for a number of reasons; including for enjoyment, to gain sensory input, or reduce sensory input, as focusing on one particular sound may reduce the impact of a loud, distressing environment something which would particularly be seen in social situations. The behaviour is also used to deal with stress and anxiety and to block out uncertainty.
Both Rotherham and Doncaster had vowed to work together to investigate the issue with a statement from the Millers also confirming that South Yorkshire Police were involved.
A statement read: "We pride ourselves on being a club that provides an environment in which everyone can enjoy football and will always operate a zero-tolerance approach to all forms of discrimination."