They were made to pay for a disappointing first half performance and couldn't recover from going 2-0 down inside 25 minutes.
No doubt stung by Spurs' win on penalties in the Ryman Cup Final a fortnight ago, where they were outplayed over the 120 minutes, Charlton stepped up a level from that night at Cheshunt as the rivals from the FA Women's Premier League clashed again.
Spurs simply could not gear near Megan Lynch's goal and whereas in the Ryman Cup Final they had a number of chances - five in the first half that night, including striking the woodwork and one off the line - it took until the 70th minute for their first shot on target this time around.
Charlton had missed chances by the time they took the lead on 11 minutes. A quick break from a Spurs attack saw Nikita Whinnett cross for Kit Graham who controlled and fired low into the corner from 16 yards.
Graham was involved again as Charlton doubled their lead 10 minutes later. Breaking through centrally, she was halted by a combination of Toni-Anne Wayne and Jenna Schillaci but the ball fell to Gemma Shepherd, who slotted home.
Katie O'Leary and Riana Soobadoo replaced Shannon Moloney and Leah Rawle at the break as chances remained few and far between, Wayne saving well one-on-one from Charley Clifford on 57 minutes.
Spurs enjoyed their best spell between the hour and 80-minute mark. Lynch did well to collect at Wendy Martin's feet, Baptiste curled a free-kick easily taken by the goalkeeper and the same player blasted another free-kick opportunity into the wall after Avilla Bergin was upended inches outside the box.
Predictably with Spurs pushing forward, Charlton secured victory on the break on 81 minutes when Graham squared for Shepherd to tap into an empty net.
Spurs will now look ahead to an apt finale of a fine season and the biggest game of the lot - the League Cup Final against Cardiff on Sunday, May 8.
Spurs Ladies: Toni-Anne Wayne, Mollie Kmita (Kelley Blanchflower 70), Alex Keown, Jenna Schillaci, Leah Rawle (Katie O'Leary 46), Shannon Moloney (Riana Soodbadoo 46), Maya Vio, Wendy Martin, Rosie Kmita (17), Avilla Bergin, Bianca Baptiste. Substitutes (not used): Chloe Morgan, Sophie McLean.