Coach Mike Shanahan said Tuesday that the fourth-round pick from Fresno State will have surgery on a torn ligament in the left foot and will require four to five months of recovery.
Shanahan said Thomas will be placed on injured reserve.
Thomas was injured in the first quarter of last week's preseason opener against the Tennessee Titans.
Thomas led all FBS players with eight interceptions last year, returning after he missed of all the 2011 season with a broken left leg and dislocated ankle. He was one of three defensive backs selected by the Redskins in April to improve a pass defense that ranked 30th last year.
Thomas was expected to see considerable playing time as a rookie. He worked frequently with the starters during training camp in place of Brandon Meriweather, who has been eased back into practice while returning from a knee injury.
Thomas started the Titans game along with fellow rookie safety Bacarri Rambo.