The 21-year-old discovered the day before the competition that she would not be allowed to compete after Team England staffers failed to complete her entry form adequately.
A subsequent appeal to the CGF was rejected and Lowther was forced to watch the race on television before going on to compete in today's road race, where she finished ninth.
"I have had an apology [from Team England]. I'm more disappointed in the Federation," Lowther told reporters afterwards. "They basically punished the rider instead of the team and I don't think that was particularly fair. Thank God my family didn't come out.
"The disappointment of the TT was hard to get over and mentally it was hard to put myself in the right place for the road race. I was all over the place mentally. One second I wanted to show them in the road race, the next I just wanted to go home. I just needed to sort my head out.
"It was a bit disappointing watching the TT knowing that's what I'd trained for all season. It's been one of the most mentally hard weeks. At first I was in shock. Then I was really angry to be honest. This has been my whole season. You don't get that many opportunities to do this sort of thing. I just need to move on from it now."
Home nation Australia completed a clean sweep of the golds in all four road cycling events on the Gold Coast.