Lewis' seven under par round of 65 put her on course for a third win of the season as she moved to 15 under par on the Senator course at the Robert Trent Jones Golf Trail's Capitol Hill complex.
Lewis, who birdied four of the first five holes in a round which included no dropped shots, said: "I think going into today I knew I needed to make birdies just the way the scores had been all day, and you don't know if you're ever going to start off like that."
Thompson had been the LPGA Tour's youngest winner when she won the title last season aged 16 but her defence faltered as a 74 dropped her into a tie for sixth on 10 under.
A defiant Thompson said: "I'm definitely not out of it. I shot 63 the first day, so if I have a round like that, I can be in contention."
Angela Stanford lies second on 13 under after shooting a 68, one stroke ahead of Lizette Salas who shot 70.
Haeji Kang and Mi Jung Hur follow at 11 under after Kang shot a 67 and Hur a 72.
Sarah Jane Smith and Hee Young Park share sixth with Thompson on 10 under after shooting 68 and 72 respectively.