The Addicks substitute fired into the ground to wrong-foot Town keeper Dean Gerken after Ipswich had led from the 23rd minute through an own goal from Richard Wood, who turned the ball into his own net following excellent work from Daryl Murphy.
The 1-1 draw saw Ipswich stretch their unbeaten run to eight matches but they were left to rue David McGoldrick's missed penalty in the second half with his side one up.
The home side started confidently and were aggrieved not to win a third-minute penalty when Murphy went down under Wood's challenge before Paul Anderson's neat curling effort was parried away by Ben Alnwick.
Charlton went close to opening the scoring in the 17th minute when Lawrie Wilson played in Yann Kermorgant whose first thought was to shoot from 25 yards. The ball deflected off Christophe Berra and zipped along the sodden turf, making Gerken's sliding tip around the post an even better save.
The deadlock was broken in the 23rd minute thanks to some excellent play down the left wing by Murphy.
His teasing low centre went across the Charlton goal and was turned in by the unfortunate Wood who could do little else.
Ipswich struggled to build on their good fortune and it was the visitors who ended the half on top.
They thought they had won a spot-kick of their own when Cameron Stewart went down under Luke Chambers' tackle but referee Stuart Attwell showed the winger a yellow card for diving in another contentious incident.
A minute before the interval, Marvin Sordell latched on to good work from Chris Solly and Kermorgant but could only fire wide from the edge of the area.
As the rain continued to pour, Paul Taylor came closest to livening up a scrappy start to the second half.
But the Ipswich forward, making his first league start for 16 months, could not find a way past Alnwick from 25 yards.
The game finally came into life in the final 15 minutes.
McGoldrick, Town's top scorer who was initially rested by manager Mick McCarthy, injected some life into proceedings, releasing Murphy whose low left-foot shot was turned away by Alnwick at his near post.
Moments later, Ipswich were awarded a penalty when Anderson went down under a barge from Jordan Cousins.
McGoldrick confidently strode up but his spot-kick was saved brilliantly by Alnwick diving to his left.
As Ipswich defended deeper, left-back Rhoys Wiggins tested Gerken from distance before the equaliser came on the stroke of the 90th minute.
Kermorgant's back-post header was teed up by Simon Church and fellow sub Jackson shot into the ground and past the stranded Town keeper.