  Magnetic skyrmions $-$ localized chiral spin structures $-$ show great
promise for spintronic applications. The recent discovery of two-dimensional
(2D) magnetic materials opened new opportunities for exploring such topological
spin structures in atomically thin van der Waals (vdW) materials. Despite
recent progress in stabilizing metastable skyrmions in 2D magnets, their
diameters are still beyond 100~nm and their lifetime, which is essential for
applications, has not been explored yet. Here, using first-principles
calculations and atomistic spin simulations, we predict that compressive
mechanical strain leads to stabilizing zero-field skyrmions with diameters
close to 10 nm in a Fe$_3$GeTe$_2$/germanene vdW heterostructure. The origin of
these unique skyrmions is attributed to the high tunability of
Dzyaloshinskii-Moriya interaction and magnetocrystalline anisotropy energy by
strain, an effect which is shown to be general for Fe$_3$GeTe$_2$
heterostructures with buckled substrates. Based on our first-principles
parameters for the magnetic interactions, we calculate the energy barriers
protecting skyrmions against annihilation and their lifetimes using
transition-state theory. We show that nanoscale skyrmions in strained
Fe$_3$GeTe$_2$/germanene can be stable for hours at temperatures up to 20 K.
