The FS1 megastar trashed Elliott and his No. 21 jersey after the RB had a rough game against the Minnesota Vikings on Sunday ... and Momma Zeke was NOT happy about it.

"I certainly hope I don’t ever see @RealSkipBayless post another pic wearing my son’s jersey," she wrote on social media.

But, Skip went on "Undisputed" on Wednesday to explain himself ... and said he's hurt that she's upset by his comments -- but he's standing by them regardless.

"Does it pain me that Momma Zeke is down? Yes, it does! Yes, it does!" Skip said. "But, I cannot tell a lie. I cannot defend her son when he doesn't deserve being defended!"

Skip says because of Elliott's fat contract ... he deserves criticism when he's not playing well, saying, "I have a job to do, and he has a $50 million guaranteed job to do on Sundays."

Skip added he's hoping he can eventually take Elliott's jersey out of his trash ... saying he wants to see a HUGE game out of the star this weekend against the Lions or next weekend against the Patriots.

As for Momma Zeke's reaction to the show? She seemed understanding of Skip's explanation ... writing on social media that she still hasn't dumped the photo of Skip and Zeke that "Undisputed" execs sent to her months ago.

"I haven’t thrown out the pic, even though MY mother asked me why it was still on my nightstand," she said.