We present a theoretical investigation of carrier-wave Rabi flopping in real atoms by employing numerical simulations of high-order harmonic generation (HHG) in alkali species. Given the short HHG cutoff, related to the low saturation intensity, we concentrate on the features of the third harmonic of sodium (Na) and potassium (K) atoms. For pulse areas of 2π and Na atoms, a characteristic unique peak appears, which, after analyzing the ground state population, we correlate with the conventional Rabi flopping. On the other hand, for larger pulse areas, carrier-wave Rabi flopping occurs, and is associated with a more complex structure in the third harmonic. These characteristics observed in K atoms indicate the breakdown of the area theorem, as was already demonstrated under similar circumstances in narrow band gap semiconductors.