Herschel/HIFI spectroscopic observations of CO J=10-9, CO J=16-15 and [CII] towards HD 100546 are presented. The objective is to resolve the velocity profile of the lines to address the emitting region of the transitions and directly probe the distribution of warm gas in the disk. The spectra reveal double-peaked CO line profiles centered on the systemic velocity, consistent with a disk origin. The J=16-15 line profile is broader than that of the J=10-9 line, which in turn is broader than those of lower J transitions (6-5, 3-2, observed with APEX), thus showing a clear temperature gradient of the gas with radius. A power-law flat disk model is used to fit the CO line profiles and the CO rotational ladder simultaneously, yielding a temperature of T_0=1100 pm 350 K (at r_0 = 13 AU) and an index of q=0.85 pm 0.1 for the temperature radial gradient. This indicates that the gas has a steeper radial temperature gradient than the dust (mean q_{dust} ~ 0.5), providing further proof of the thermal decoupling of gas and dust at the disk heights where the CO lines form. The [CII] line profile shows a strong single-peaked profile red-shifted by 0.5 km s-1 compared to the systemic velocity. We conclude that the bulk of the [CII] emission has a non-disk origin (e.g., remnant envelope or diffuse cloud).