Although this animation isn't traditional frame-by-frame like the works of the old masters either, it was still made by a real human artist, Mathias Lynge, using After Effects.
If you're an After Effects user, we've previously featured a whole collection of Ghibli-inspired pieces by Seter MD, including Star Children and two beautifully crafted watereffects:
Mathias is considering making a process video if there's enough interest and also offers a full course on mastering stroke-based motion design, which covers the ripple effect in this animation. Follow him on LinkedIn for updates, and check out some of his After Effects tutorials: