I've also constructed an Axes object programmatically using the OO interface and a basic plot command works as expected.

import matplotlib
matplotlib.use('pdf')
from matplotlib.figure import Figure
from matplotlib.backends.backend_pdf import FigureCanvasPdf as figcan

fig = Figure()
can = figcan(fig)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.plot([1, 2, 3])
fig.savefig('asdf.pdf')

3D axes also works using the usual from mpl_tookits.mplot3d import Axes3D and setting the projection on the ax object.

Notice the repr (or str, I can never remember which one) has changed to <matplotlib.axes._axes.Axes at 0x10a0b91d0>. That said, it's reasonable for us to assume that people don't depend on that output.