Aims. We investigate the physical properties and spatial distribution of Carbon Monoxide (CO) gas in the disks around the Herbig Ae/Be stars HD 97048 and HD 100546. Methods. Using high-spectral-resolution 4.588-4.715 μm spectra containing fundamental CO emission taken with CRIRES on the VLT, we probe the circumstellar gas and model the kinematics of the emission lines. By using spectro-astrometry on the spatially resolved targets, we constrain the physical size of the emitting regions in the disks. Results. We resolve, spectrally and spatially, the emission of the 13CO v(1-0) vibrational band and the 12CO $v = 1{-}0$, $v = 2{-}1$, $v = 3{-}2$ and $v = 4{-}3$ vibrational bands in both targets, as well as the 12CO $v = 5{-}4$ band in HD 100546. Modeling of the CO emission with a homogeneous disk in Keplerian motion, yields a best fit with an inner and outer radius of the CO emitting region of 11 and ${\geq}$100 AU for HD 97048. HD 100546 is not fit well with our model, but we derive a lower limit on the inner radius of 8 AU. The fact that gaseous OI emission was previously detected in both targets at significantly smaller radii suggests that CO may be effectively destroyed at small radii in the surface layers of these disks.