Bernard, who snatched the record from Olympic champion Pieter van den Hoogenband at the Dutchman's home pool in Friday's semifinals, lowered it by a further 0.10 to 47.50 seconds to win the final by the best part of a second.
Bernard had clocked 47.60 seconds in the semis to beat the 47.84 mark Van den Hoogenband set in the last four of the 2000 Sydney Olympics on the way to the first of his two Olympic 100 freestyle titles.
The heavily-muscled Bernard turned at the 50-metre mark in 22.53, a breathtaking 0.35 seconds inside his own world record split of 22.88, and powered down the return length to finish the job to the cheers of spectators in the National Swimming Centre.
Sweden's Stefan Nystrand took silver in 48.40. Italy's world champion Filippo Magnini bronze in 48.53.
Russia maintained their winning ways and claimed two of the day's three other pool titles. Yuri Prilukov won the 1500 freestyle for the fourth time in a row, completing his second consecutive European 400 and 1500 golden double but complaining that the water was too warm.
Russia's 15-year-old Yulia Efimova won the women's 200 breaststroke in a championship record of two minutes 24.09 seconds from 100 breaststroke champion Mirna Jukic of Austria (2:24.58). Team mate Alena Alekseeva added bronze to her 100 silver.