We report on the amplitude and phase modulation of picosecond optical pulses, near λ = 800 nm, transmitted through sub-wavelength rectangular apertures in thin gold films with thicknesses of λ/10 at per-pulse energies of <0.3 nJ or 9 pJ per aperture. Due to the excitation and strong confinement of surface plasmon polaritons in the apertures, the leading edge of a pulse causes a rapid heating of the electrons and lattice to modulate its falling edge. By comparing cross-correlation frequency resolved optical gating measurements with simulations, the thermal effects responsible for the induced pulse dynamics are identified.