A goal in either half from Kian Scales and Andy Cook mean that Bradford City leave the JobServe Community Stadium with all three points, despite Frank Nouble's first half equaliser.
Bradford City took the lead in the opening ten minutes after a good effort from Kian Scales found the top corner of Gerken's net.
But Colchester United fought back late on in the first half with Frank Nouble's header, although they could not press on from their strong finish to the first forty-five as the Bantams retook the lead.
Andy Cook's second half header was enough for all three points as the U's fell to a 2-1 defeat.
Wayne Brown named an unchanged starting eleven to the side that were held to a 2-2 draw in the week against Tranmere Rovers, but did make a switch on the substitues bench.
Rem Oteh was missing from the matchday eighteen, and replaces on the subs bench by Tom Lapslie, who returns to the squad after recovering from a persistent injury.
It was a bright start from Colchester United who had a chance to open the scoring in the opening minute with Brendan Sarpong-Wiredu. From Jevani Brown's knock down, Brendan struggled to get the ball under control before taking the shot that was easily saved by O'Donnell.
But the Bantams quickly grew into the game and had a chance themselves in the opening five minutes of the match. A cross from the left flank was hit high towards Andy Cook in the centre, who saw his downward header blocked in the six-yard area before Eastman was able to clear.
The visitors made their early pressure count in front of goal as they took the lead with ten minutes on the clock. It was Kian Scales on target for the Bantams, curling in a well hit effort from the edge of the box into the top corner of the net.
Despite having the ball for the majority of the next fifteen minutes, the U's were struggling to create any clear cut chances in and around the Bradford City penalty area. Looking to get back on level terms, Jevani Brown's back post header forced a good save out of O'Donnell, but the United forward pushed his man to win the ball and the pressure was relieved on the visitors.
The U's looked like they would be the most likely team to score the next goal and equalise, creating chances down both wings.
Courtney Senior put in some great work on the right wing before looking up and laying the ball towards Jevani Brown, but the U's front man was unable to keep his effort down as O'Donnell watched the ball over the bar.
Harry Pell was the next man to have a chance, when Frank Nouble raced down the left flank this time. He got away from his man before spotting the U's captain in the centre of the area with Pell just unable to guide the ball into the back of the net.
But United deservedly got themselves back on level terms three minutes before the half-time whistle. Jevani Brown's whipped cross from a free kick was measured perfectly for Frank Nouble to nod the ball back across goal and into the net, making it 1-1.
Wayne Brown's side were the only ones who looked as though they might take the lead before the break. In the third minute of stoppage time, Jevani Brown brilliantly controlled the ball in the six-yard box before having the ball taken off his toe by Canavan.
Senior looked to be fouled as he collected the ball in the penalty area just before half-time, but the referee decided it was no penalty as the teams headed to the dressing rooms level.
After the break it was Colchester United who again looked the most likely to find the net. Harry Pell and Frank Nouble drilled balls into the area and were unlucky to see them cleared or blocked before a U's man was able to get a touch to it.
But despite their early second half pressure, it was the visitors who retook the lead. Good work from Clayton Donaldson on the left wing meant he was able to cross to Andy Cook who guided his header calmly into the corner of the net.
The U's had to try and find a way to get back on level terms once again, and had a good chance with captain Harry Pell from the edge of the area. Courtney Senior's step overs worked the space before Pell smashed the ball high over the bar from just outside the area.
A minute later the Bantams rattled the crossbar through the man who opened the scoring, Kian Scales. From a tight angle his right footed effort beat Gerken, but not the bar with Evans unable to latch onto the follow up as the ball bounced away.
For all the U's late pressure, they were unable to break through the solid Bantams' defence and snatch an equaliser, as Wayne Brown and Hayden Mullins' side fell to a 2-1 defeat.
The defeat means that Colchester United remain in twenty-first position thanks to a late winner from Stevenage against Barrow.
The U's next opponents, Bolton Wanderers beat Forest Green 1-0 earlier today to go fourth in the table.
Colchester United starting XI: Gerken, Smith, Senior, Pell, Brown (Cowan-Hall 83'), Eastman, Clampin (Doherty 55'), Sarpong-Wiredu (Chilvers 83'), Stevenson (Lapslie 61'), Tchamadeu, Nouble.
Unused subs: George, Welch-Hayes, Folivi.
Bradford City starting XI: O'Donnell, P O'Connor, Canavan, A O'Connor, Donaldson (Foulds 90'), Evans, Sutton, Wood, Cousin-Dawson (Watt 63'), Scales (Stevens 90'), Cook (Rowe 79').
Unused subs: Hornby, Burrell, Shanks.