Williams finished 1min 20.07sec behind gold medallist Grace Brown (Australia), and a shade over 45sec behind second-placed Anna Henderson of England.
Williams is missing a race with her trade team, Team BikeExchange - Jayco, in order to attend the Games and says she felt a bit of pressure to get on the podium to prove it was worth it.
The 28-year-old said she rode as well as she could have.
"It was really tough - it was a super hard course, super technical," she said.
"There was always something to focus on, whether it was a corner, a hill or a descent. But it did make it fun."
New Zealand's Mikayla Harvey finished 20th and Henrietta Christie pulled out on the morning of the race feeling unwell.
Williams said the bronze medal was a boost ahead of the 112km road race on Sunday.
She took silver in the road race at the last Commonwealth Games and knew she was one of the favourites in Birmingham.
"I'm one of the strongest, so I need to play to my strengths.
Later, triple gold medallist Aaron Gate finished just outside the medals in the road time trial.
Gate, who won gold on the track in the team and individual pursuit, and the points race, finished fourth in the 37km event, which was won by Australian Rohan Dennis, 26 seconds ahead of England's Fred Wright.
Welshman Geraint Thomas grabbed the bronze, despite crashing his bike into the barriers
