The striker pounced five minutes from time to cancel out Billy Sharp's early opener for Scunthorpe.
Hayter seized upon a rebound after Scunthorpe keeper Tom Evans had saved from substitute James Coutts.
Sharp's goal on six minutes came in fortunate circumstances.
He robbed full-back Callum Hart and raced down the right touchline before crossing for Steve Torpey. However, Bournemouth keeper Gareth Stewart mis-judged the flight of the ball and it sailed over his head before crashing against the far post and into the back of then net.
Sharp then proceeded to run back up the line and celebrate in front of the 100 or so away fans that had made the trip south.
Hayter nearly pulled one back for Bournemouth on 33 minutes when a quickly taken Brian Stock free-kick landed in his path but his right-foot effort was well saved by Evans.
Hayter then squandered Bournemouth's best chance of the half on 38 minutes when James O'Connor set him up only to head against the bar from six yards out.
Scunthorpe seemed intent on preserving their 1-0 lead and failed to muster any real opportunities in the second period.
It was left to Bournemouth to provide the attacking play and Hayter again came close three minutes into the second half when he cut inside and forced a good save from Evans.
Dani Rodrigues then when close with a speculative volley which he miscued from five yards out enabling Richard Hinds to clear off the line.
Bournemouth though were finally rewarded for all their attacking endeavour when Hayter scored with time running out.