Meester played Carrie in the TV series, which ran from 2004 to 2007, but she wasn't available to play the character in the upcoming film version, prompting Thomas to cast Estella -- the lead singer of one of his favorite bands, Twin Sister -- in the part, TVGuide.com reported.
"Sadly, [Meester] was doing a different movie during the same time frame on the wrong coast. In the end, she was unavailable," Thomas told the movie's Kickstarter backers in an e-mail Sunday.
"We needed a performer who could sing in this important role," Thomas said. "[So I] decided to cast someone from a band I already wanted in the movie."
"It's been a bit of dream to be in a movie, especially being a messed-up rock princess," Estella said in a statement. "How could I say no? I think the 'VM' fans are going to be very happy!"
"Veronica Mars" regulars Kristen Bell, Jason Dohring and Enrico Colantoni have already signed on for the movie. Thomas raised the film's nearly $6 million budget through a Kickstarter fan-contribution campaign.
2014: The Year in Music [PHOTOS]