Mikele Leigertwood's first goal for Reading had put the npower Championship side in control but Darius Charles appeared to have earned the hosts a replay with a 78th-minute goal.
But Long grabbed his ninth goal in as many games with just three minutes left to put the Royals into round five.
The npower League Two side had beaten Newcastle in round three, but they failed to reach those heights as the Royals made it through.
Source: PA
Source: PA