The drug, that will be on sale by the end of the year, will be handed out to people who have tested positive for Chlamydia which can cause infertility if left untreated.
It is thought one in 10 young people have the disease, which can have no symptoms at all.
For the first time it will be possible to be tested and treated for a sexually transmitted disease without having to see a doctor.
It is hoped more people will be diagnosed and treated because of the convenience of visiting a pharmacist instead of a GP or hospital sexual health clinic and it is hoped more medicines for a wide variety of conditions will follow.
The move will not change guidance from the National Institute for health and Clinical Excellence which recommends that antibiotics not be prescribed for cough, colds, and sore throats, experts said.
Antibiotics are effective against Chlamydia and patients must be treated quickly in order to avoid further spread, they said.
Patients will be able to buy an approved standard testing kit, called Clamelle costing £25, post a urine sample to an approved laboratory where the test will be carried out and receive the results back in the post with information and advice.
If the test is positive, the patient goes to any pharmacy, not necessarily the same one where the test was bought, and the results are confirmed via computer.
If the patient has no other symptoms then the pharmacist will hand out the antibiotic, called azithromycin costing £20, with instructions on its use, and take details of sexual partners so they can be traced and tested.
If the patient has symptoms they will be advised to see their GP as they might have another disease as well as Chlamydia.
The drug will be available to anyone over the age of 16 for themselves and their partner from December.
Azithromycin was previously only available on prescription from doctors and the Medicines and Healthcare products Regulatory Agency (MHRA) has now changed its status so it can be supplied by pharmacists.
Dr June Raine, Director of Vigilance and Risk Management of Medicines at the MHRA said: "Chlamydia is the most common sexually transmitted disease in the UK. Up to 70% of people who have Chlamydia have no symptoms and could therefore remain undiagnosed. This means that they are at huge risk of serious long-term health complications, including infertility and ectopic pregnancy.
"Today's (wed) move means that symptom–free people diagnosed with Chlamydia and their partner will be able to get convenient effective treatment from their local pharmacy."
She said the MHRA is hoping to allow more medicines to be supplied through pharmacies where it is safe to do so.
Colette McCreedy, National Pharmacy Association's Chief Pharmacist said: "The NPA supports this reclassification wholeheartedly as we believe community pharmacies are ideally placed to offer Chlamydia screening and treatment. We also believe that the proposed pharmacy service will complement existing provision within the NHS and will help to ease the financial restrictions and overstretched resources currently affecting existing services for this rapidly escalating problem."
Tests for Chlamydia are also available through the national screening programme along with free treatment for those aged under 25 and all patients can still visit their GP or genito-urinary clinic as well.
Antibiotic creams and eye drops for cold sores and conjunctivitis are already available from pharmacists but this is thought to be the first time anywhere in the world that an oral antibiotic tablet has been made available without prescription.
