We investigate the formation of double-peaked asymmetric line profiles of CO in the fundamental band spectra emitted by young (1–5 Myr) protoplanetary disks hosted by a 0.5–2 M☉ star. Distortions of the line profiles can be caused by the gravitational perturbation of an embedded giant planet with q = 4.7 × 10−3 stellar-to-planet mass ratio. Locally isothermal, two-dimensional hydrodynamic simulations show that the disk becomes globally eccentric inside the planetary orbit with stationary ∼0.2–0.25 average eccentricity after ∼2000 orbital periods. For orbital distances 1–10 AU, the disk eccentricity is peaked inside the region where the fundamental band of CO is thermally excited. Hence, these lines become sensitive indicators of the embedded planet via their asymmetries (both in flux and wavelength). We find that the line shape distortions (e.g., distance, central dip, asymmetry, and positions of peaks) of a given transition depend on the excitation energy (i.e., on the rotational quantum number J). The magnitude of line asymmetry is increasing/decreasing with J if the planet orbits inside/outside the CO excitation zone (RCO ⩽ 3, 5, and 7 AU for a 0.5, 1, and 2 M☉ star, respectively), thus one can constrain the orbital distance of a giant planet by determining the slope of the peak asymmetry–J profile. We conclude that the presented spectroscopic phenomenon can be used to test the predictions of planet formation theories by pushing the age limits for detecting the youngest planetary systems.