The loudspeaker announcements were made following a court order.
A group of men allegedly beat up the 17-year-olds last week after they came out of an internet cafe in Kattankudi, a mostly Muslim town.
The father of one of the girls says they were accused of watching pornography – a charge the girls deny.
Mohammad Yusuf Abdul Razak told the BBC that the issue had been blown out of proportion because of an earlier announcement made from mosque loudspeakers that that two girls had been viewing pornography.
Mr Razak said that a group of men forcefully took his daughter and the other girl to a local house and beat them up, before taking them to a local Islamic office.
“After that, an announcement was made from a mosque using loudspeakers that two girls were caught doing wrongful things,” Mr Razak said.
After hearing this announcement, Mr Razak says, a large crowd gathered and started to denounce the girls.
Police finally intervened and the girls were taken to hospital for treatment for their injuries, he said.
Local Muslims deny making announcements regarding the girls from a mosque. But they agreed on Wednesday to comply with court orders to broadcast the exonerations.
“Today we made announcement from about eight or nine mosques covering the whole area of the Kattankudi town,” said Mosque Federation Chairman Mohammad Ibrahim.
“The crux of the message is the girls have not been found guilty of any wrongdoing and are innocent. Local people should help those girls and their family to live in peace.”
Police are yet to trace the main accused. But Mr Razak said that he was happy with the retraction.
“I want to thank the judge for restoring our honour,” he said.
By Swaminathan Natarajan /BBC Tamil
Mosques in the eastern Sri Lankan town of Kattankudi have made public announcements exonerating two teenage girls accused of watching pornography.