The Spaniard had been almost half a second clear of the field when he went down heavily on the exit of turn four, bringing his session to a premature conclusion 12 minutes from the end.
Despite missing the late running, Espargaro's best of 1:35.191s proved enough to hang on to pole for the final race of the season.
Newly-crowned champion Marc Marquez was Espargaro's nearest challenger on the track, although he was guaranteed to start at the back of the field following a penalty for a practice collision.
In the end that proved no influence on the pole fight however, with the Monlau Suter man unable to match Espargaro.
Marquez also fell five minutes from the end, but was able to get his bike restarted and even improved on his final lap - although he was still more than four tenths off pole.
No other rider was able to get within half a second of the benchmark time, with Thomas Luthi - third in the session and therefore second on Sunday's grid - 0.565s in arrears.
The Swiss rider can still catch Andrea Iannone, who starts from ninth, for third place in the championship.
Takaaki Nakagami claimed the final share of the front row, with Nico Terol, Jordi Torres and Dominique Aegerter rounding out the top six.
In what was a relatively low-key session, Scott Redding claimed seventh ahead of Simone Corsi and Iannone.
Bradley Smith was only 22nd in his final Moto2 qualifying session before stepping up to the Tech3 MotoGP squad.