Margate started well and put the visitors under early pressure with Adeboyejo and Scott Donnelly forcing the visitor’s keeper Dimitar Mitov into early saves. Bull’s side thought they had taken the lead after 20 minutes as Donnelly’s superb in-swinging corner was hacked off the line by the young Addicks back line.
Charlton created their first real chance of the evening shortly after as Karl- Ahearne Grant saw his fierce low drive well collected by Valery Pajetat in the Blues goal.
Margate took the lead on 37 minutes after some really neat play which saw Donnelly slip Adeboyejo through who superbly lobbed the on-rushing Mitov to give the Gate a deserved lead at the break.
The second half started very much the same with Margate controlling proceedings but being unable to secure a second goal that would have killed the game off as Adeboyejo and Daniel Akindayini saw chances come and go within quick succession.
Charlton should have levelled in the 78th minute as Ahearne-Grant saw his effort superbly saved by Pajetat low down to his right as Margate looked to hold onto for a win that would have been so deserved.
Margate were just seven minutes away from triumph when Charlton grabbed an equaliser through substitute Mikhail Kennedy as fired home from a low cross to bring the scores level.
Just as both sides were preparing to head to penalties, Charlton grabbed a last minute winner as Ahearne-Grant side footed past Pajetat from six yards out to give Charlton the win and send them through to the semi-finals.
Margate are back in Vanarama National League South action on Saturday as they travel to Hungerford Town with kick off at 3pm.
MARGATE: Pajetat, Taylor, Fox, Phipps, Johnson ©, Moore-Azille, Richefond, Donnelly (Rowland 83’), Adeboyejo, Akindayini, Banya
Subs not used: Foster, Kallmeier, Williams, Heffernan
Man of the Match: Lewis Taylor