We describe Doppler spectroscopy of Bose-Einstein condensates of ytterbium atoms using a narrow optical transition. We address the optical clock transition around 578 nm between the ${^1}S_0$ and ${^3}P_0$ states with a laser system locked on a high-finesse cavity. We show how the absolute frequency of the cavity modes can be determined within a few tens of kHz using high-resolution spectroscopy on molecular iodine. We show that optical spectra reflect the velocity distribution of expanding condensates in free fall or after releasing them inside an optical waveguide. We demonstrate sub-kHz spectral linewidths, with long-term drifts of the resonance frequency well below 1 kHz/hour. These results open the way to high-resolution spectroscopy of many-body systems.