Charles, 56, and Parker Bowles, 57, emerged on Saturday to the cheers of a large crowd shortly before 1pm (1200 GMT) after a civil ceremony lasting about 20 minutes.
The couple headed back from Windsor town hall to a religious blessing in nearby Windsor Castle conducted by Archbishop of Canterbury Rowan Williams.
The marriage, which was attended by Charles' two sons, Princes William and Harry, but not by his mother, the queen, comes eight years after the death of his first wife, Princess Diana.
Diana blamed Parker Bowles for contributing to the break-up of her marriage, and polls indicate a large majority of Britons oppose the idea of her becoming queen.
Security was extra tight around Windsor, 40km west of London along the River Thames, with marksmen on rooftops and officers mingling with the crowd, estimated by police at about 15,000. There were no reports of any incidents.
The public was never intended to see any of the ceremony, which was originally going to have been held securely behind the castle walls before a hitch emerged over wedding licences.
The couple are to honeymoon in Scotland.