Karen Hills’ side suffered their first away league defeat of the season after goals from Ellie Hack and Paula Howell’s cancelled out Kiera Skeels’ first-half header.
Despite a strong start from the Addicks, the hosts found themselves ahead inside five minutes after a Lewes corner was met by Hack's head and found the back of the net.
Charlton then went searching immediately for an equaliser Beth Roe came close in the 13th minute when she swung a ball into the box which curled over the bar.
But with 17 minutes on the clock, the Addicks deadlock was broken when defender Kiera Skeels buried her header home from the Charlton corner.
Hills’ side continued to press, Angela Addison found some space down the flank and the pacey forward broke into the box and took a strike, but it only found the gloves of Sophie Whitehouse.
Charlton racked up a number of corners in the first half with both Emily Simpkins and Ella Rutherford sharing the duty of putting the deliveries into the box, but due to some resolute defending from the hosts and super stops by Whitehouse between the sticks the Addicks were put on hold to find their second goal.
The Rooks then had an effort of their own on target in the 38th minute but the strike was straight into the arms of Sian Rogers.
Freda Ayisi very nearly put the Addicks ahead in the final moments of the first half, but her strike was deflected and saved by Whitehouse.
Shortly after the interval, Lewes found themselves in the lead again after Paula Howell's strike beat Rogers.
The second half saw Charlton create more chances which where equally matched by some resolute defending. Elisha N’Dow came close to levelling at the hour mark when her header from the corner was tipped onto the crossbar.
Tegan McGowan was brought into play just after the hour mark and the young forward injected some additional energy into Charlton creating some additional chances of her own.
Charlton shot stopper Rogers made a solid save ten minutes from time when Lewes were awarded a free kick just outside the box, Palmer’s shot swung around the wall and was gathered by the keeper.
Charlton continued to press right up until the final moments of the game, but Hills’ side just could not find a way through and the game ended in a narrow defeat.
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Charlton: Rogers, N'Dow, Johnson, Simpkins (McGowan 65), Ayisi, Addison, Skeels, Rutherford, Roe (O'Rourke 79), Henson, Ross
Subs: Soper, Bashford, O'Rourke
Goals: Skeels (17)
Booked: Skeels 54'
Lewes: Whitehouse, Mason, Cleverly, Hazard, Hack, Johnson, Palmer, Kraft Stobbs, Howells, McKenna,
Subs: Moore, Thompson, Pizzarello, Rita, Smith, Heria, Copus-Brown, Longhurst, Dalton
Goals: Hack (5), Howells (53)
Booked: Johnson 62'