Do you mean was actually pronounced? We have a pretty good idea. Frances Lord, a professor of Latin at Wellsley College discusses this issue in The Roman Pronunciation Of Latin: Why We Use It and How To Use It (Boston: Ginn, 1893).
A slightly older friend in parochial school was in his third or fourth year of Latin when the curriculum switched from teaching ecclesiastical pronunciation (basically Italian) to classical pronunciation.
He mulled it all over, raised his hand and said, "Sister, I REFUSE TO BELIEVE that Julius Caesar said 'WANEY-WEEDY-WEEKY!'"
bump for later
I would have guessed an obscure little institution known as the Roman Catholic Church just might’ve kept the pronunciations alive, maybe...