The 21-year-old was the only rider to break the 50-minute barrier over the 43.5km route between Pistoia and Florence.
"There were no secrets, just going fast on the flat course," last year's bronze medallist said.
"I won the Australian and Oceania time trials this year and I set these worlds as my next goal."
Howson will also be part of the Australian team in Friday’s road race.
1. Damien Howson (Australia) 49:49
2. Yoann Paillot (France) +57
3. Lasse Hansen (Denmark) +1:10
4. Campbell Flakemore (Australia) +1:22
5. Lawson Craddock (USA) + 1:41
6. Stefan Kueng (Switzerland) + 1:46
7. Ryan Mullen (Ireland) + 1:47
8. Victor Campenaerts (Belgium) + 1:48
9. Danil Fominykh (Kazakhstan) + 2:05
10. Eduardo Sepulveda (Argentina) + 2:10