A big second-half was needed from the Eagles in order to make the comeback, and a change in formation during halftime saw Leigh Nicol make way for Bianca Baptiste.
The south Londoners came out looking stronger and nearly equalised just one minute after kick-off as Shiv Wilson made a tremendous run down the line, however her shot was eventually blocked by the Lewes defence.
The visitors continued with high intensity, looking to double their lead - and they nearly did so in the 60th-minute through Georgia Timms, but her shot flew wide over the bar.
Palace then immediately fought back; Lizzie Waldie’s long range pass found Molly Sharpe up top. She picked out Bianca Baptiste in the box and she slotted the ball past the Lewes ‘keeper to level the game.
The goal changed the game in Palace’s favour and the team began to play with much better intensity, spending greater time in the Lewes box.
Just 10 minutes later, a mistake by the Lewes defence allowed Baptiste to find Wilson in the box who tapped in the second goal for the Eagles, giving the home side an all-important lead.
The Rooks continued to fight back and were close to levelling the game in the 85th-minute. Ashworth- Clifford managed to take a shot on goal from the edge of the box but it flew above the crossbar.
An additional three minutes of time were added onto the game, and it looked like it would finish 2-1. However, a foul from Lewes ‘keeper Tatiana Saunders on Coral Haines saw her sent off and the Eagles awarded a penalty deep into stoppage time.
Lewes then bought on their second ‘keeper, ex-Palace player Shanell Salgado, to face the penalty, but Haines sent her the wrong way to give Palace a 3-1 lead with the full-time whistle blown shortly after.
Next up Palace travel away to the Robins High Performance Centre to face Bristol City Women on Sunday, 6th February, looking to continue their winning streak in the Women’s Championship.
Crystal Palace: Orman, Johnson, Cowan, Everett, Waldie, Pearse, Wilson, Nicol (Baptiste 45), Sharpe (Hennessy 76), McLean, Barton (Haines 85).
Subs not used: Smith, Coombs, Sibley, Clifford, Churchill
Lewes: Saunders (Salgado 90+3), Mason, Hazard, Cousins, Ashworth- Clifford, Timms, Howells (Logan 80), McKenna, O'Rourke, Dalton (Nobel 81) , Cross (Porter 80)
Subs not used: Cleverly, Cordier, Longhurst