A second-half strike from Freda Ayisi wrapped up the three points for the Addicks on a rainy Wednesday evening at The Oakwood.
A game of few chances that showed the odd spark was settled 18 minutes from time after an Ayisi shot was deflected past keeper Sophie Whitehouse as the Addicks move up to third in the Barclays Women's Championship.
It was a cagey opening 20 minutes before the clash really started to look like it would hot up.
Former Addick Amber-Keegan Stobbs had the opening chance two minutes into the contest, but Sian Rogers got down well to save. It took a good 12 minutes for Charlton to have their first sniff, but the ball ran too far from Sophie O’Rourke to get contact.
The game sparked into life about 10 minutes later when Lewes had a half-hearted appeal for a penalty turned down by the referee. Up the other end, a succession of chances came and went for the hosts.
A searching ball over the top from O’Rourke was latched onto by Freda Ayisi, but the attacker could only volley over the bar. Moments later, Johnson got one-on-one with Sophie Whitehouse, albeit from a tight angle, but the Lewes keeper did well to parry it out for a corner at her near post.
Beth Roe’s resulting corner bent dangerously goalwards and Whitehouse had to be alert again to claw it away from underneath the crossbar and out for another set piece. That presented another great chance for the home side, but Elisha N’Dow couldn’t get enough on it to beat Whitehouse.
An Emily Simpkins free kick that was just out of the reach of Keira Skeels floated agonisingly close to the far post but, in true style of the way the first period went, the final quarter rather fizzled out.
Charlton started the second half on the front foot, with Addison looking the most likely to break the deadlock. The winger fired a few curled efforts on goal that were dealt with by Whitehouse. She then fed Lauren Bruton with a square pass that was drilled but saved again.
Lewes had a great chance on the hour mark as the ball fell for Rhian Cleverly, but Rogers made a stunning fingertip save to deny her and keep the score level.
Ayisi then struck with 72 minutes on the clock, sliding goalwards and seeing her shot deflect off a defender and in.
The game became even more scrappy as the visitors searched for an equaliser, with three players going into the book including Charlton skipper Simpkins and stopper Rogers.
With five minutes of stoppage time having been played, Lewes had a gilt-edged chance to level up the clash and break Charlton's hearts when a ball into the area found substitute Emma Thompson on her own in the box, but she could only flash the ball well wide of goal.
Charlton: Rogers, N’Dow, Johnson (Follis 71), Simpkins, Ayisi, Bruton, Addison, Skeels, Roche (Ross 59), O’Rourke, Roe
Subs (not used): Gray, Lindbaek, Hennessy, Logan, Bashford, Henson
Lewes: Whitehouse, Mason, Cleverly (Weir 77), Hazard (Dalton 77), Wardlaw, Johnson (Thornton 84), Palmer (Copus-Brown 77), Stobbs, Howells (Mushtaq 74), Barton, McKenna.
Subs (not used): Kraft, Rita, Longhurst, Dalton, Moore.
Goal: Ayisi, 71