Blackman had another effort a few minutes later as a left-wing cross found him in the box, but he ballooned his volley high over the bar.
© Getty Images
After a quiet period, Danny Williams forced Walker into a finger-tip save later in the half as the away side took control of possession and started to threaten, but they could not find the breakthrough.
Colchester started the second period in positive fashion as Tom Eastham's header from a corner was blocked close to goal, before being hooked away by the Reading defence.
Reading came closest to scoring in the first half of extra time too, as Blackman's thundering effort hit the crossbar, before Chris Gunter was released through on goal and he found the bottom corner.
Colchester piled men forward in search of an equaliser, but Reading held on to secure victory.