Handler was widely reported to have publicly criticised Jolie during a comedy set earlier this month, accusing the actress of breaking up Aniston's marriage to Brad Pitt.
Days later, she continued to denounce Jolie as "insincere".
PopEater reports that Aniston has taken the decision to distance herself from Handler as a result of the comments.
"Jen and Chelsea haven't officially fallen out but they certainly won't be going on vacation together for a long time unless Chelsea promises to never talk about Angelina again," a source close to Handler told Rob Shuter.
"She understands that what Chelsea did was out of loyalty, but it didn't help. In fact, it made things worse."
A friend of Aniston echoed the comments, saying: "Jen is a very private person.
"It's one thing to crash Angelina in private; it's another to do it in public. Chelsea should have known better and is feeling Jen's cold shoulder for her mistake."