The Shrimpers seemed set for all three points when midfielder Kevan Hurst thundered them in front with a scorching long-range shot in the 73rd minute.
But, just two minutes from time, Mullins bundled the ball home at the back post after a goalmouth scramble to ensure Rotherham picked up a point.
The two teams, who are both challenging for play-off positions in npower League Two, played out an uneventful first half with a Daniel Nardiello header that Southend goalkeeper Paul Smith tipped over the best chance of the opening 45 minutes.
That meant the Shrimpers have still not scored in the first half of a home league game since September.
But they were on top at the start of the second period with Britt Assombalonga going close with a header that Andy Warrington did well to smother.
Hurst then fired Southend in front from distance but Mullins' scrappy late leveller meant it was not the game's winning goal.