Well, I should have tried one more thing before posting. Using PyPlot directly works:
julia> using PyPlot
julia> ax1=subplot(2,1,1)
PyObject <matplotlib.axes._subplots.AxesSubplot object at 0x12c6d6fd0>
julia> plot(randn(100,1))
1-element Array{PyCall.PyObject,1}:
PyObject <matplotlib.lines.Line2D object at 0x139bb3dd0>
julia> ax2=subplot(2,1,2, sharex=ax1)
PyObject <matplotlib.axes._subplots.AxesSubplot object at 0x139c0fcd0>
julia> plot(randn(100,1))
1-element Array{PyCall.PyObject,1}:
PyObject <matplotlib.lines.Line2D object at 0x139c49c90>