From the way it looked moving across the sand, I'd agree -- looked more like animation overlay. But when it went over the shuttle, it looked like it had a CGI effect.
I rewatched the scene on Netflix, and it looked to me like they just used the outline of the 2D-animated blob as a moving split screen line between a shot of the uncovered shuttle and a shot of it coated in black goo. It's definitely not a 3D effect.