We study two microscopic models of topological insulators in contact with an $s$-wave superconductor. In the first model the superconductor and the topological insulator are tunnel coupled via a layer of scalar and of randomly oriented spin impurities. Here, we require that spin-flip tunneling dominates over spin-conserving one. In the second model the tunnel coupling is realized by an array of single-level quantum dots with randomly oriented spins. It is shown that the tunnel region forms a $pi$-junction where the effective order parameter changes sign. Interestingly, due to the random spin orientation the effective descriptions of both models exhibit time-reversal symmetry. We then discuss how the proposed $pi$-junctions support topological superconductivity without magnetic fields and can be used to generate and manipulate Kramers pairs of Majorana fermions by gates.
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