Until then the in-form visitors Southend had looked set to snatch all three points after their leading marksman Lee Barnard headed them in front from a corner in the 48th minute with his sixth goal of the season.
Former Southend striker Gary Hooper was anxious to impress against his former club and twice went close before testing goalkeeper Adam Federici midway through the first half.
But Hooper missed a real sitter on the stroke of half-time when he headed wide of an open goal after a mistake by Federici.
Scunthorpe were stunned as the visitors took an early second-half lead with virtually their first effort of the game.
As Scunthorpe tried to hit back Hayes missed two clear-cut opportunities and centre-back David Mirfin headed over from almost point-blank range.
But the equaliser finally came in controversial fashion when a linesman spotted a shirt pulling offence in a crowded box and Hayes stepped up to drill his spot-kick passed Federici for his seventh goal of the season.
It was tough luck on Southend who stretched their own unbeaten run to seven games.
Former Southend striker Gary Hooper was anxious to impress against his former club and twice went close before testing goalkeeper Adam Federici midway through the first half.
But Hooper missed a real sitter on the stroke of half-time when he headed wide of an open goal after a mistake by Federici.
Scunthorpe were stunned as the visitors took an early second-half lead with virtually their first effort of the game.
As Scunthorpe tried to hit back Hayes missed two clear-cut opportunities and centre-back David Mirfin headed over from almost point-blank range.
But the equaliser finally came in controversial fashion when a linesman spotted a shirt pulling offence in a crowded box and Hayes stepped up to drill his spot-kick passed Federici for his seventh goal of the season.
It was tough luck on Southend who stretched their own unbeaten run to seven games.