This approach may be brittle (tested with pandas 0.11.0), but you could iterate over the axes.patches list. A more reliable approach would be to build the bar plot yourself with calls to plt.barh(). (side note: very small alphas were invisible, so I set the minimum alpha to .2)
from itertools import product
ax = df[['m4_params','m5_params','m6_params']].T.plot(kind='barh')
for i, (j, k) in enumerate(product(range(3), range(3))):
patch = ax.patches[i]
alpha = 1 - df[['m4_pvalues','m5_pvalues','m6_pvalues']].T.iloc[j, k]
patch.set_alpha(max(alpha, .2))
plt.draw()