A Team England official failed to tick a box on her entry form, meaning Lowther was not formally entered for the race. Team England lost an appeal to have Lowther included.
The 21-year-old was informed of the mistake the day before the race and is “gutted” to have missed out.
“While Team England has apologised, I’m still gutted not to have the opportunity to represent my country after all the hard miles I’ve put in,” said Lowther.
“I can’t put into words how disappointed I am to have been missed off the start list due to an admin error.”
England’s chef de mission Sarah Winckless apologised to Lowther and the cycling coaches.
“Melissa has trained hard for and focused on this race and it should never be the case that an error on our part prevents an athlete showing what she can do,” Winckless said.
The Commonwealth Games Federation said there had been no chance of the decision being overturned.
“The rules are very strict,” CGF chief executive David Grevemberg said. “England has a very big team. These things happen.”
Lowther will still be eligible to compete in Saturday’s road race.