The Cherries eased into a two-goal lead but were left stunned when home goalkeeper Scott Flinders headed in a late leveller. However, Leyton Orient's loss to Tranmere means Bournemouth are guaranteed a top-six spot.
Striker Steve Lovell was played in by the influential Harry Arter and he angled a low finish across Flinders that beat Neil Austin on the line to make it 1-0.
Flinders, however, should have kept out the second goal after 39 minutes. Winger Donal McDermott, on loan from Manchester City, fired in a low shot from 25 yards that squirmed under his body and into the net.
Pools looked well beaten but when Leon McSweeney was held back by Anton Robinson, Adam Boyd made no mistake from the penalty spot after 52 minutes.
Lovell and Liam Feeney both hit the woodwork in a frantic scramble, but Pools had their chances to level. And it came in injury time when Flinders powered in a header from eight yards.