Having created the better chances, it looked like the team was going to lose 1-0 only for substitute Leah Rawle to find an equaliser in the 90th minute to take the game into extra time.
However, just when you thought momentum would be with the home side, Charlton's Kit Graham pinged her second 20-yarder of the night into the top corner to hand the Addicks the lead again five minutes into the added 30.
Rosie Kmita hit the post with seven minutes remaining but there were no more last-gasp heroics this time around and Charlton lifted the trophy.
Playing in front of a packed crowd at Wodson Park, Spurs found their passing game tricky on a firm, bouncy surface but nevertheless tore into their first cup final since 2012 with real zest.
However, they were jolted with a goal out of the blue from the visitors on 17 minutes. Charlton broke over halfway and were clinical with player advantage as Gemma Shepherd found Graham, who drove to the edge of the box before firing into the top corner. Shepherd soon broke again but lobbed wide.
At the other end, Spurs' best chances came via set-pieces and skipper Jenna Schillaci's excellent delivery. She provided a corner headed over by Lucia Leon, a free-kick that met the same fate from Wendy Martin and then another corner in injury time that Katie O'Leary looked to have planted home only for her header to come back off the post.
Into the second half and but for a Kim Dixson free-kick touched onto the crossbar by Toni-Anne Wayne on the hour, it was all Spurs.
Bianca Baptiste, who starred down the right flank throughout, saw a shot deflected narrowly wide and Leon headed Schillaci's corner straight at Megen Lynch, who then produced a fine save to turn around Maya Vio's low drive.
Schillaci curled a free-kick just over with five minutes remaining but Spurs kept going and with the clocking ticking into the 90th minute, Schillaci's free-kick was played back into the danger area by Baptiste and Rawle forced home from close range.
You felt if Spurs could take the lead in extra time they would have one hand on the trophy but the crucial next goal went to Charlton, a carbon-copy of their opener. This time Spurs lost possession on halfway and Graham again drove to the right corner of the box before again finding a finish worthy of a cup final into the top corner.
Clear-cut chances were at a premium but a moment of magic from Baptiste sparked the final onslaught on 111 minutes as she controlled a pass with her right foot and swept between two defenders before hitting a dipper just over with her left foot.
Two minutes later and the final chance. Martin flicked on Sophie McLean's cross from the right and Kmita wrapped her foot around a volley from 10 yards that agonisingly cannoned back off the post.
If that had gone in we were all set for a grandstand finish, but it wasn't to be.
Spurs Ladies: Toni-Anne Wayne; Lucia Leon (Rosie Kmita, 72), Alex Keown, Jenna Schillaci (C), Sophie McLean; Maya Vio, Wendy Martin, Riana Soobadoo (Shannon Maloney, 62); Avilla Bergin, Katie O'Leary (Leah Rawle, 86), Bianca Baptiste. Unused subs: Laura Picton (gk), Leanne Mabey, Andra Marcoci.
Charlton Ladies: Megen Lynch, Katie Flack, Stef Simmons (Emma Harrison, 93), Kim Dixson (C), Rosie Paye (Ruby Southgate, 108), Grace Coombs, Charley Clifford, Sam Pittuck, Gemma Shepherd, Nikita Whinnett (Amy Howlett, 110), Kit Graham. Unused sub: Katie Hardaker.