Bournemouth needed to pick up at least a point and hope Bradford, the only team who could catch them, failed at Chesterfield.
While Bradford went on to lose, Bournemouth made sure of safety with a hard-earned point.
Gillingham, already safe, had the better of the first half and it was no surprise when they took the lead in the 24th minute with a header from Andrew Crofts from a right-wing centre by Craig Stone.
But Bournemouth drew level when Shaun Cooper found Hayter unmarked on the edge of the area and his low right-foot shot gave Simon Royce no chance of saving.
Both teams had plenty of opportunities to have snatched a win.
But Stephen Purches, Steve Fletcher and Darren Anderton all missed for Bournemouth.
At the other end, Gareth Stewart made important stops from Danny Jackman, Mark Bentley and Michael Flynn.
Bournemouth manager Kevin Bond raised his arms in triumph at the final whistle at the end of nine months battling relegation.
Bond said: "James Hayter produced a quality finish and his goal came at the perfect time for us just before the break."
Gillingham manager Ronnie Jepson was away scouting and left team affairs to his assistant Mick Docherty.