Gardasil, which will be used in the UK HPV vaccination campaign from September 2012, will protect schoolgirls aged 12-13 against 90% of genital warts as well as 70% of cervical cancers.
It will replace the Cervarix vaccine, which only protects against cervical cancer.
The move was welcomed by sexual health doctors.
The decision comes after a survey by charity British Association for Sexual Health and HIV (BASHH) earlier this year found most sexual health professionals backed a switch to Gardasil.
Professor David Salisbury, DoH director of immunisation, said: 'We have one of the best HPV vaccination programmes in the world and we want that success to continue.
'It will be tremendous to see rates of cervical cancer falling. The number of women getting abnormal results from HPV screening will also fall. Many women will no longer have to live through the worry and stress of follow-up after screening, including treatment for precancerous lesions.'
The bivalent Cervarix vaccine has been used in the HPV vaccination programme since it began in 2008. It protects against HPV types 16 and 18, which cause 70% of cervical cancers.
Gardasil protects against HPV types 6 and 11, which cause 90% of genital warts cases, in additiion to types 16 and 18.
Cervarix manufacturer GSK said it chose not to bid for the contract after the government decided to give increased priority to genital warts in the tender.
Dr Tony Falconer, president of the Royal College of Obstetricians and Gynaecologists, said: 'We are delighted that the DoH has decided on the quadrivalent vaccine.
'Not only will it provide immunity against cervical cancer caused by HPV, it will also protect against the strains of HPV that cause genital warts, which are unpleasant and the cause of much psychological distress for sufferers.'
GSK said the latest figures showed more than 84% of girls aged 13-14 had received all three doses of Cervarix.
Professor Salisbury said those who had already had the vaccine did not need to be vaccinated again.