Christopher Prather, 20, of Lancaster, was charged Friday with burglary and sexual battery after entering the apartment of the 21-year-old woman Feb. 11.
Sgt. Mark Machanic says Prather watched the woman sleep. When she woke up, he whispered "excuse me," groped her and fled. The flip-flops were later discovered and sent to a lab for testing. Prather was arrested Tuesday, just hours after lab results were returned to Lancaster officials.
Prather was already on felony probation for robbery. He is being held on $170,000 bail.
The Associated Press contributed to this report.