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.