The Millers completely dominated a one-sided first half, but not for the first time this season, they failed to turn their superiority into goals.
However, they looked on course for the win when Kieran Agard fired them ahead, only for Ryan Lowe to deny them with a late penalty.
Tranmere had 10 men behind the ball at every hint of danger, but despite a hatful of chances, the hosts could not find the back of the net in a one-sided first half. The nearest they came was a Tom Eaves header from Ben Pringle's corner which was headed off the line by Max Power.
But after Rotherham were denied a clear 60th-minute penalty the deadlock was broken a minute later. Ben Pringle's ball into the box found Agard and he turned and shot past Owain Fon Williams.
But after denying Rotherham a penalty, referee Tony Cleveland gave one to Tranmere after 84 minutes for a Pablo Mills push on substitute Abdulai Bell-Baggie and Lowe equalised from the spot.
Matt Tubbs had a chance to win it for the hosts but he dragged a late shot wide of the post.