Rotherham rested leading scorer Adam Le Fondre but the home side started brighter and went in front in the first period when Lewis Hunt latched on to Scott Dobie's flick-on and fired into the corner past Andy Warrington.
Winger Marcus Marshall equalised before the break with a well directed header at the far post over stranded 'keeper Lenny Pidgeley.
The Millers stepped up the pace after the break with Pidgeley making three fine stops, the best of which from Johnny Mullins, whilst Callum Kennedy hit the crossbar with a left footed free-kick.
But after having a goal disallowed, Adeyemi fired a powerful 25-yard injury time effort that seemed to hit the crossbar and bounce back into play, only for the assistant referee to award the goal as the game ended in controversy.