The Grease star shared the video on Dec. 25. It features Ella and Ben in front of a Christmas tree surrounded by presents.
"Say Merry Christmas," John says in the video, to which Ella and Ben respond "Merry Christmas!" with smiles and waves.
This year will certainly be different for the Travolta kids, who lost their mom Kelly in July after a two-year battle with breast cancer. The actress, who starred in movies like What a Girl Wants, Sky High, and Gotti alongside her husband, was 57.
John shared the sad news "with a heavy heart" in a lengthy Instagram caption.
"She fought a courageous fight with the love and support of so many," he shared alongside a photo of Kelly. "My family and I will forever be grateful to her doctors and nurses at MD Anderson Cancer Center, all the medical centers that have helped, as well as her many friends and loved ones who have been by her side. Kelly's love and life will always be remembered. I will be taking some time to be there for my children who have lost their mother, so forgive me in advance if you don't hear from us for a while. But please know that I will feel your outpouring of love in the weeks and months ahead as we heal."
The Christmas video is the actor's first Instagram post since Thanksgiving, where he spoke directly to the camera.
"I just want to take this moment to thank each and every one of you for supporting me in such an incredible way this year," he said. "Happy Thanksgiving, and always love."
In August, the Hairspray star shared a sweet Instagram video of him and Ella dancing in honor of Kelly.
"My daughter @ella.travolta and I dancing in memory of momma," he wrote. "One of Kelly's favorite things, dancing with me."
While the family has suffered a tremendous loss, it seems that they have each other to lean on during this unprecedented holiday season.