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The energy damping time in a mechanical resonator is critical to many precision metrology applications, such as timekeeping and force measurements. We present measurements of the phonon lifetime of a microwave-frequency, nanoscale silicon acoustic cavity incorporating a phononic bandgap acoustic shield. Using pulsed laser light to excite a colocalized optical mode of the cavity, we measured the internal acoustic modes with single-phonon sensitivity down to millikelvin temperatures, yielding a phonon lifetime of up to [Formula see text] se