After two overs' play on Sunday, Rogers crouched down by the side of the pitch and then sat motionless.
Concerned batting partner David Warner signalled for medical staff to come out on to the field and after a few minutes' treatment, Rogers, who had added five runs to his overnight score, walked off on 49 not out, with Australia 114 without loss.
The 37-year-old Rogers, who has said he plans to retire after the end of this series, received sympathetic applause from a packed crowd at Lord's, where he spent several seasons with Middlesex, as he made his way into the Pavilion.
Rogers missed Australia's recent 2-0 series win in the Caribbean with concussion after being hit on the head while batting in the nets.
And during the first innings of this match, during his Test-best 173, Rogers was struck flush on the side of the helmet by James Anderson when he turned his head away from the opening ball of Friday's second day.
Rogers's place in the middle was taken by Steve Smith, whose first-innings 215 was also his highest score in Tests. England lead the five-match series 1-0 after their 169-run win in the first Test in Cardiff last week.