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Gillingham conceded a last-minute penalty as they were denied a much-needed win on Saturday.
Bradley Dack headed the Gills infront just before the break.
Substitute keeper Stuart Nelson kept Gillingham ahead with several top-class saves in the second half, including denying Ricky Holmes from the penalty spot.
Charlton levelled with a second penalty, in the last minute, scored by Nicky Ajose.
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It was a goal all the more frustrating for the Gills who had two big shouts for penalties themselves turned down.
Referee Mark Haywood made a number of questionable decisions throughout and he took much of the flak from Gills fans on the final whistle.
Reaction: Assistant boss believes the Gills should have had at least one penalty
Gillingham had ended a run of three straight defeats in the league with a midweek point against Walsall, described by under-fire boss Justin Edinburgh as ‘something to build on’.
They were so close to getting back to winning ways on Saturday with a performance that was much improved.
Visitors Charlton weren’t much better off than the Gills prior to the meeting at Priestfield – the first since 2009 – having struggled to adapt to life outside the Championship.
Only goal difference separated the sides who were both sitting just a point off the relegation zone.
They remain on the same points following Saturday’s action.
Both managers went into the game under pressure from their respective fans.
Edinburgh named an attacking line-up, returning both Jay Emmanuel-Thomas and Frank Nouble to the starting XI, flanking inform striker Cody McDonald in a 4-3-3 formation.
Gillingham took the lead late in the half and earned the advantage with plenty of positive play, much of it coming from Emmanuel-Thomas.
The Gills forward had a hand in the opening goal but provided the ammunition for a couple of other good chances. He released Ryan Jackson to run at goal with a cross/shot that sailed just over.
Dack was seeing plenty of the ball and his 26 minute chance was even better, in on goal from an Emmanuel-Thomas pass but was denied by keeper Declan Rudd.
Charlton lacked potency upfront but they had their chances. Nelson saved from Josh Magennis after the forward attempted to prod home Ademola Lookman’s free-kick.
Nelson was back between the sticks after replacing Jonathan Bond, who limped off with another groin injury with 30 minutes gone,
Gillingham took a deserved lead in the 41 minute. Emmanuel-Thomas switched play from right to left and a cross from Paul Konchesky was headed home by Dack, for his third goal of the season.
Charlton changed shape for the second half, replacing midfielder Johnnie Jackson for striker Nicky Ajose, but the Gills started the better. Billy Knott twice fired well wide before Emmanuel-Thomas had a low shot saved.
Nelson took centre-stage around the hour mark. A super reflex save denied Magennis as his header looked destined for the top corner and moments later – after Jackson had conceded a penalty with a tug on Fredrik Ulvestad – he pushed away Holmes’ spot-kick.
The Gills were twice denied penalties in the space of five minutes with McDonald twice impeded inside the area. Haywood was unwilling to even things up.
Home keeper Nelson was kept busy at the other end, with another great save to turn away Ezri Konsa’s shot, after a corner had been cleared towards the edge of the area.
Dack almost doubled the lead with a trademark burst into the box, getting onto the end of Nouble’s cut-back but flashing a shot just wide.
With a minute left Chris Herd was adjudged to have handled in the box and Haywood pointed to the spot. Substitute Ajose made no mistake as he sent Nelson the wrong way to level things up.
Referee Haywood came under fire from fans on the final whistle as his decisions proved crucial.
Gillingham: Bond (Nelson 30mins), Jackson (Osadebe 84mins), Konchesky, Herd, Ehmer, Hessenthaler, Knott, Dack, Nouble, Emmanuel-Thomas, McDonald. Subs not used: Donnelly, Pask, Oldaker, List, Byrne.
Charlton: Rudd, Solly, Fox, Holmes, Konsa, Pearce, Crofts, Jackson (Ajose 46mins), Lookman, Ulvestad, Magennis (Novak 78mins). Subs not used: Phillips, Foley, Lennon, Hanlan, Teixeira.
Attendance: 8,670 (2,360 away)