Optical frequency combs based on mode-locked lasers have revolutionized the field of metrology and precision spectroscopy by providing precisely calibrated optical frequencies and coherent pulse trains. Amplification of the pulsed output from these lasers is very desirable, as nonlinear processes can then be used to cover a much wider range of transitions and wavelengths for ultra-high precision, direct frequency comb spectroscopy. Therefore full repetition rate laser amplifiers and enhancement resonators have been employed to produce up to microjoule-level pulse energies. Here we present a spectroscopic method to obtain frequency comb accuracy and resolution by using only two frequency comb pulses amplified to the millijoule pulse energy level, orders of magnitude more energetic than what has previously been possible. The new properties of this approach, such as cancellation of optical light-shift effects, are demonstrated on weak two-photon transitions in atomic rubidium and caesium, thereby improving the frequency accuracy by up to thirty times.