Matplotlib's autoscale doesn't seem to work on y axis for small values?

I believe this is a known issue which is still not solved in matplotlib. It is the same as here or here.

Possible solutions for this case would be

Use plot instead of scatter.

import matplotlib.pyplot as plt

y=  [1.09E-05,  1.63E-05,   2.45E-05,   3.59E-05,   5.09E-05,   6.93E-05,   9.07E-05]
x=  [0, 10, 20, 30, 40, 50, 60]

fig3, ax3 = plt.subplots()
ax3.plot(x, y, color='k', marker = "o", ls="")
ax3.autoscale(enable=True, axis="y", tight=False)
plt.show()

Use invisible plot in addition to scatter

import matplotlib.pyplot as plt

y=  [1.09E-05,  1.63E-05,   2.45E-05,   3.59E-05,   5.09E-05,   6.93E-05,   9.07E-05]
x=  [0, 10, 20, 30, 40, 50, 60]

fig3, ax3 = plt.subplots()
ax3.scatter(x, y, color='k', marker = "o")
ax3.plot(x, y, color='none')
ax3.relim()
ax3.autoscale_view()
plt.show()

Manually scale the axis using set_ylim.

import matplotlib.pyplot as plt

y=  [1.09E-05,  1.63E-05,   2.45E-05,   3.59E-05,   5.09E-05,   6.93E-05,   9.07E-05]
x=  [0, 10, 20, 30, 40, 50, 60]

fig3, ax3 = plt.subplots()
ax3.scatter(x, y, color='k', marker = "o")

dy = (max(y) - min(y))*0.1
ax3.set_ylim(min(y)-dy, max(y)+dy)
plt.show()