Young stars' near-infrared emission shows several puzzling features: variability uncorrelated with visible-light changes, foreground extinction that recurs erratically on weekly timescales, and excesses over the stellar photosphere too large to explain by reprocessing in a hydrostatic protostellar disk. I examine whether these features can be explained by a time-varying, magnetically-supported disk atmosphere like those suggested by MHD calculations of magneto-rotational turbulence. Through Monte Carlo radiative transfer calculations I demonstrate that such an atmosphere yields near-infrared variations spanning the observed range of amplitudes. Since the starlight-absorbing surface lies higher than in hydrostatic models, a greater fraction of the stellar luminosity is reprocessed into the near-infrared, offering a natural explanation for the larger excesses. The atmosphere rises high enough to obscure the star in systems viewed near edge-on, provided the dust in the outer parts of the disk has undergone some growth or settling.