The visitors started brightly and went close when Gary Liddle volleyed over before Charlton's leading marksman Bradley Wright-Phillips saw a snapshot go just wide after being picked out by skipper Johnnie Jackson.
Injury forced Jackson to make way for Danny Haynes with half an hour played and within a minute the visitors took the lead as Peter Hartley tapped past Ben Hamer from Neil Austin's corner.
Hamer did well to save Austin's stinging free-kick early in the second half, while Wright-Phillips saw a volley fly over after strike partner Yann Kermorgant cleverly headed the ball into his path.
Charlton were level in the 70th minute when Danny Hollands met Rhoys Wiggins' corner with a volley. Scott Flinders made a fine one-handed stop to deny Kermorgant but there was nothing the Hartlepool keeper could do to prevent Haynes heading the host's in front on 78 minutes.
A stunning goal at the far post by Kermorgant extended the advantage three minutes later as the French forward finished from the tightest of angles. And even though Liddle's deflected 86th minute strike pulled one back for the visitors, it was too late to prevent the champions finishing the season on a winning note.