Weeraratne, 24, created the record on Tuesday playing for Ragama cricket club against Kurunegala in Sri Lanka's premier limited-overs tournament.
The effort surpassed England all-rounder Adam Hollioake's half-century off 15 balls for Surrey against Yorkshire at Scarborough in 1994.
Weeraratne ended on an unbeaten 66 off 18 balls, an innings studded with eight sixes and two boundaries.
He took five successive sixes and a boundary in one over from 40-year-old left-arm spinner Ajith Ekanayake.
"I did not know it was a record until I heard it in the news," said Weeraratne, who represented Sri Lanka in 11 one-day internationals before being dropped.
Weeraratne's feat, however, ended in vain as the match ended in a no-result due to rain.
Sri Lanka's senior squad is trailing 0-3 in a seven-match one-day series in India.
Another Sri Lankan, Sanath Jayasuriya, holds the record for the fastest half-century in one-day internationals. He made 50 off 17 balls against Pakistan in Singapore in April, 1996.