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We investigate the interplay of magnetic fluctuations and Cooper pairing in twisted bilayer graphene from a purely microscopic model within a large-scale tight-binding approach resolving the Ångström scale. For local onsite repulsive interactions and using the random-phase approximation for spin fluctuations, we derive a microscopic effective pairing interaction that we use for self-consistent solutions of the Bogoliubov-de-Gennes equations of superconductivity. We study the predominant pairing types as function of interaction strength, temperature and band filling. For large regions of this parameter space, we find chiral $d$-wave pairing regimes, spontaneously breaking time-reversal symmetry, separated by magnetic instabilities at integer band fillings. Interestingly, the $d$-wave pairing is strongly concentrated in the AA regions of the moiré unit cell and exhibits phase windings of integer multiples of $2π$ around these superconducting islands, i.e. pinned vortices. The spontaneous circulating current creates a distinctive magnetic field pattern. This signature of the chiral pairing should be measurable by state-of-the-art experimental techniques.