We solve analytically and numerically the generalized Einstein equations in scalar-tensor cos- mologies to obtain the evolution of dark energy and matter linear perturbations. We compare our results with the corresponding results for minimally coupled quintessence perturbations. Our results for natural (O(1)) values of parameters in the Lagrangian which lead to a background expansion similar to CDM are summarized as follows: 1. Scalar-Tensor dark energy density perturbations are amplified by a factor of about 104 compared to minimally coupled quintessence perturbations on scales less than about 1000h−1Mpc (sub-Hubble scales). This amplification factor becomes even larger (& 106) for scales less than 100h−1Mpc. On these scales dark energy perturbations constitute a fraction of about 10% compared to matter density perturbations. 2. Scalar-Tensor dark energy density perturbations are anti-correlated with matter linear perturbations on sub-Hubble scales. Thus clusters of galaxies are predicted to overlap with voids of dark energy. 3. This anti-correlation of matter with negative pressure perturbations induces a mild amplification of matter perturbations by about 10% on sub-Hubble scales. 4. The evolution of scalar field perturbations on sub-Hubble scales, is scale independent and therefore it corresponds to a vanishing effective speed of sound (cs = 0). It also involves large oscillations at early times induced by the amplified effective mass of the field. This mass amplification is due to the non-minimal coupling of the field to the Ricci curvature scalar and (therefore) to matter. No such oscillations are present in minimally coupled quintessence perturbations which are suppressed on sub-Hubble scales (cs = 1). We briefly discuss the observational implications of our results which may include predictions for galaxy and cluster halo profiles which are modified compared to CDM . The observed properties of these profiles are known to be in some tension with the predictions of CDM .