However, Superdrug says the fact that the pills would have to be paid for by credit or debit card means that under-age girls could not use the service.
Superdrug was forced to back down by the Department of Health and the Royal Pharmaceutical Society.
The company had only just announced the drug's availability on the internet a few hours previously.
Superdrug decided to temporarily suspend the scheme and await the outcome of discussions to review the protocol surrounding the supply of the product.
The Department of Health had expressed concerns that an internet delivery service could detract from the prescriber's ability to evaluate how well the woman understood what taking the drug meant and the prescriber's ability to offer contraceptive advice for the future.
The DoH is also concerned that the drug may become available to teenagers under 16.
However, Superdrug says the fact that the pills would have to be paid for by credit or debit card means that under-age girls could not use the service.
Under new guidelines, introduced earlier this month, the morning-after pill is available over the counter, but not to any woman under 16 years of age.
Superdrug.com is the first site that proposes to allow women to be able to order emergency contraception.
If their scheme is finally allowed to proceed, Levonelle will cost £19.99 and customers within the M25 will be offered an express door-to-door delivery service costing an extra £7.50.
The controversial move would have meant women being able to have the drug delivered to their door within hours of placing their order.
Superdrug has spelt out what it says are safeguards for the sale of the drug.
Their reassurances were not enough, however, for the DoH and the Royal Pharmaceutical Society.
Superdrug's internet proposals provoked a mixed response earlier in the day
A spokesman for the anti-abortion charity, Life, said: "It can only serve to promote promiscuity and add to the already rampant sexually transmitted disease epidemic that is affecting so many of our young people.
"We must not forget that the primary function of Levonelle is to abort. It destroys life."
Amanda Callaghan, of the British Pregnancy Advisory Service, said emergency contraception should be available on-line.
She said: "Wider availability of emergency contraception will be of great benefit to many women who are currently not able to access it when they need it."
The Superdrug U-turn comes as the House of Lords defeated an attempt to stop the morning-after pill being sold over-the-counter.
The government recently decided to allow sales of the drug in pharmacies, without a doctor's prescription.
Campaigners have already attacked the relaxation of the rules.