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We consider the effective two-Higgs-doublet potential with complex parameters, when the $CP$ invariance is broken both explicitly and spontaneously. Diagonal mass term in the local minimum of the potential is constructed for the physical basis of Higgs fields, keeping explicitly the limiting case of $CP$-conservation, if the parameters are taken real. For special case of the two-doublet Higgs sector of the minimal supersymmetric model, when $CP$ invariance is violated by the Higgs bosons interaction with scalar quarks of the third generation, we calculate by means of the effective potential method the Higgs boson masses and evaluate the two-fermion Higgs boson decay widths and the widths of rare one-loop mediated decays $H\rightarrow \gamma \gamma$, $H\rightarrow gg$.