We report results from joint NuSTAR, Swift and XMM-Newton observations of the newly discovered black hole X-ray binary candidate Swift J1658.2-4242 in the intermediate state. We observe a peculiar event in this source, with its X-ray flux rapidly decreasing by $sim$45% in $sim$40~s, accompanied by only subtle changes in the shape of the broadband X-ray spectrum. In addition, we find a sudden turn-on of a transient QPO with a frequency of $6-7$~Hz around the time of the flux change, and the total fractional rms amplitude of the power spectrum increases from $sim$2% to $sim$10%. X-ray spectral and timing analyses indicate that the flux decrease is driven by intrinsic changes in the accretion flow around the black hole, rather than intervening material along the line of sight. In addition, we do not significantly detect any relativistic disk reflection component, indicating it is much weaker than previously observed while the source was in the bright hard state. We propose accretion disk instabilities triggered at a large disk radius as the origin of the fast transition in spectral and timing properties, and discuss possible causes of the unusual properties observed in Swift J1658.2-4242. The prompt flux variation detected along with the emergence of a QPO makes the event an interesting case for investigating QPO mechanisms in black hole X-ray binaries.