Leeds went into the League One game on the back of three successive defeats in all competitions, including the shock 1-0 reverse at Conference side Histon in the FA Cup.
But despite a slow start, they opened the scoring in the 34th minute when Robert Snodgrass fired home from 12 yards with his fourth goal of the season.
Snodgrass had another opportunity two minutes before the break with James Walker again equal to the task before Colchester levelled on the stroke of half-time.
Yeates swung over a corner and Dean Hammond headed past goalkeeper David Lucas to collect only his second goal of the season.
The visitors then went ahead in the 66th minute after Prutton was given his marching orders following a second yellow card for a foul on Yeates, who struck the resulting free-kick into the top corner from 20 yards.