Under the change, visitors will be issued tickets with a return time and a shorter wait similar to the FastPass system that's offered to everyone.
The current way "certainly has been problematic, and we wanted to curb some of the abuse of this system," Disneyland Resort spokeswoman Suzi Brown told the Orange County Register.
The change takes effect Oct. 9 for guests with park-issued disability cards. Disney officials said more details will be released after park employees are briefed on the new rules.
Currently, visitors unable to wait in the regular line can get backdoor access to rides or go through the exit and wait in a shorter line.
Brown compared the change to making a reservation and boarding at the appointed time.
The move was a response to the phenomenon of disabled "tour guides" who charge money, sometimes hundreds of dollars, to accompany able-bodied guests and allow them to avoid long lines.
The park said others who don't have a disability have been able to get an assistance card since no proof of disability is required.
Some families of children with epilepsy and autism criticized the change, saying some kids' disabilities just don't allow them to wait in standard lines.
"Given the increasing volume of requests we receive for special access to our attractions, we are changing our process to create a more consistent experience for all our guests while providing accommodations for guests with disabilities," Brown said in a statement.
Rebecca Goddard takes her sons, age 4 and 6, to Disneyland once a week. Her sons have autism and can't stand in lines longer than a few minutes before they start pushing other people.
"My boys don't have the cognition to understand why it's going to be a long wait," Goddard told the Register. "There are so few things for my boys that bring them utter joy and happiness — to mess with it just makes me sad."
The advocacy group, Autism Speaks, consulted with Disney officials on the change and urged parents to see how it unfolds.
"Change is difficult," said Matt Asner, executive director of the Southern California chapter. "I didn't want it to change, but I understand there was an issue that needed to be dealt with."