You get a three sphere by gluing two solid tori along their boundary by the mapping class group element S. You can get a Hopf link by filling each core of the two solid tori with a line operator. Thus, the (full) braiding phase between quasiparticles a and b is computed as
$\langle T^2, a | S | T^2, b \rangle$,
where the state $|T^2, a\rangle$ is the state on the torus obtained by performing the open path integral over the solid torus with the a line in its core.