The Addicks fall to defeat in the opening fixture of the Continental Cup after a late Lewes goal in each half secured the victory for the home side.
Charlton created the first opportunity of the afternoon when Emily Simpkins came charging down the wing and swung a low cross into the area, but the danger was cleared by Emily Moore.
The Addicks then came forward again and earned a free-kick, the skipper looped the cross in and both Angela Addison and Tegan McGowan pounced onto the ball which pin balled inside the area for a while but was eventually cleared away.
Shortly after Lewes were then awarded a free kick of their own, but Charlton dealt with the threat well thanks to some resolute defending.
The visitors then came forward again and this time McGowan set up Kiera Skeels who had a strike from range, but it was comfortably gathered from Moore.
Sophie O’Rourke then darted down the wing for Charlton and crossed in a threatening ball but this time it was straight into the arms of the Lewes keeper.
The Rooks then came blazing down the middle of the park, Ellie Mason took the shot this time, but it blazed over.
At the 35-minute mark, Melissa Johnson looped an impressive ball into McGowan, but some impressive Rooks defending saw the ball get knocked away from the forward before she had the chance to shoot.
Three minutes before the interval Lewes took the lead, goalkeeper Poppy Soper who made her Charlton debut got down to her right and produced an impressive first save, but the ball rebounded out to Paula Howells who slotted home.
Charlton posed the first attack after the break. Corinne Henson sent in an impressive corner ball delivery, but it just couldn't find an Addicks head.
The visitors continued to press in search of an equaliser with both Addison and McGowan creating opportunities, but the pair were quickly closed down by The Rooks.
At the 75-minute mark, Mary Bashford came on to make her Continental Cup debut.
Ten minutes from time Amber Keegan-Stobbs tried her luck from 30-yards but her shot blazed over. Shortly after Taylor Bell came on to make her Charlton debut.
In stoppage time The Rooks doubled their lead after the corner ball was headed in by Ellie Hack.
The Addicks will return to league action after the international break to host Blackburn Rovers on Sunday, October 16th at The Oakwood, click here for tickets.
Charlton: Soper, N’Dow, Johnson, Simpkins, Addison (Logan 60), Skeels, O’Rourke, Roe (Bell 89), McGowan (Bashford 74), Henson, Ross (Ayisi 60)
Subs (Not used): Rogers
Booked: O’Rourke 90+
Lewes: Moore, Mason, Cleverly, Hack, Johnson, Palmer, Stobbs, Thompson, Howells, McKenna, Dalton
Subs: Whitehouse, Angel, Hazard, Pizzarello, Rita, Smith, Heria, Copus-Brown, Longhurst
Goals: Howells (42), Hack (90+)
Referee: C. Small
Attendance: 403