ABSTRACT Hot Jupiters might reside inside the Alfvén surface of their host star wind, where the stellar wind is dominated by magnetic energy. The implications of such a sub-Alfvénic environment for atmospheric escape are not fully understood. Here, we employ 3D radiation-magnetohydrodynamic simulations and Ly-$\alpha$ transit calculations to investigate atmospheric escape properties of magnetized hot Jupiters. By varying the planetary magnetic field strength ($B_\mathrm{p}$) and obliquity, we find that the structure of the outflowing atmosphere transitions from a magnetically unconfined regime, where a tail of material streams from the nightside of the planet, to a magnetically confined regime, where material escapes through the polar regions. Notably, we find an increase in the planet escape rate with $B_\mathrm{p}$ in both regimes, with a local decrease when the planet transitions from the unconfined to the confined regime. Contrary to super-Alfvénic interactions, which predicted two polar outflows from the planet, our sub-Alfvénic models show only one significant polar outflow. In the opposing pole, the planetary field lines connect to the star. Finally, our synthetic Ly-$\alpha$ transits show that both the red-wing and blue-wing absorptions increase with $B_\mathrm{p}$. Furthermore, there is a degeneracy between $B_\mathrm{p}$ and the stellar wind mass-loss rate when considering absorption of individual Ly-$\alpha$ wings. This degeneracy can be broken by considering the ratio between the blue-wing and the red-wing absorptions, as stronger stellar winds result in higher blue-to-red absorption ratios. We show that, by using the absorption ratios, Ly-$\alpha$ transits can probe stellar wind properties and exoplanetary magnetic fields.