The seven times world champion's Mercedes team had requested an exemption after Hamilton's self-scrutineering sheet failed to confirm he was complying with a requirement to remove all jewellery.
The ban on jewellery during a race is for safety reasons and is set out in the FIA's International Sporting Code, but it was not rigorously enforced until last season when it triggered headlines.
Hamilton has worn a permanent nose stud in his left nostril for years and photographs in Bahrain have shown him also with one on the right.
He explained at last October's Singapore Grand Prix, when he was also given an exemption, that taking the left one out had caused the piercing to become infected.
The stewards in Bahrain said in a statement they had consulted the FIA medical delegate who examined Hamilton and agreed with the request for a continued exemption.
"We have determined to take no further action as there are concerns about disfigurement with frequent attempts at removal of the device," the stewards explained.
The rules state that "the wearing of jewellery in the form of body piercing or metal neck chains is prohibited during the competition and may therefore be checked before the start."
