Combining LSDA+$U$ and an analysis of superexchange interactions beyond DFT, we describe the magnetic ground states in rutile and anatase Cr-doped TiO$_2$. In parallel, we correct our LSDA+$U$ ground state through GW corrections ($GW$@LSDA+$U$) that reproduce the position of impurity states and the band gaps in satisfying agreement with experiments. Because of the different topological coordinations of Cr-Cr bonds in the ground states of rutile and anatase, superexchange interactions induce either ferromagnetic or antiferromagnetic couplings of Cr ions. In Cr-doped anatase, this interaction leads to a new mechanism which stabilizes a ferromagnetic ground state, in keeping with experimental evidence, without the need to invoke F-center exchange.