With England striker Ivan Toney again absent following more speculation over his future this week, Thomas Frank watched Keane Lewis-Potter put the visitors ahead in contentious fashion on the stroke of half-time.
Sky Bet League Two club Colchester wanted a foul for Kevin Schade’s push on Aaron Donnelly but nothing was given by referee Paul Howard and it allowed Lewis-Potter to walk in the opener.
Fans in the South Stand at the JobServe Community Stadium were told in an announcement over the PA system on the 77th minute to stop “racist, homophobic and sexist chanting”.
Four minutes later, Colchester were given a penalty but Jack Payne’s low effort was saved by Valdimarsson with his feet to send the Premier League club through to round three.
Icelandic goalkeeper Valdimarsson was also handed a first start and endured some nervy early moments, struggling with Donnelly’s long throw which saw Tom Hopper go close.
After a bright start by Colchester, Brentford started to settle and only a superb block by Ben Goodliffe denied Carvalho a goal midway through the half after fine work by right-back Ryan Trevitt.
Lewis-Potter’s influence on the left was also beginning to grow and he headed wide from a corner before Carvalho curled straight down the throat of Matt Macey from 22 yards.
It looked set to be goalless at the break but Brentford broke the deadlock on the verge of half-time in controversial fashion.
Schade battled with Donnelly, who went down in the penalty area after seemingly getting a shove, but play continued and it allowed the Brentford forward to set up Lewis-Potter for a simple goal.
Colchester were stunned as boos echoed around the stadium and home boss Danny Cowley made his feelings known on the touchline.
Chants of ‘1-0 to the referee’ followed as Howard walked off the pitch after Cowley ushered his players away from the official.
The sting was taken out of the white-hot atmosphere by two separate injury stoppages for the impressive Bradley Ihionvien and Milton Oni.
Ihionvien continued and was booked with 19 minutes left when he reacted furiously after a tangle with last-man Ben Mee failed to result in a free kick.
It sparked chants of “the referee’s a racist” from Colchester’s noisy South Stand.
Supporters in that section were told to stop “racist, homophobic and sexist chanting” after a police officer spoke with fourth official Ruebyn Ricardo.
Colchester were awarded a penalty when Frank Onyeka brought down substitute Mandela Egbo.
Referee Howard immediately pointed to the spot but Colchester’s joy was short-lived with Payne’s penalty down the middle saved by the feet of Valdimarsson, who proved to be the Bees’ hero.
Brentford’s Controversial Win
Brentford rode their luck at both ends of the pitch to reach the third round of the EFL Cup at League Two Colchester’s expense.
At the end of a disjointed, uneventful first-half at the Colchester Community Stadium, Keane Lewis-Potter slotted the Bees ahead after Aaron Donnelly had gone to ground under Kevin Schade's challenge.
Having taken the lead in controversial fashion, the Bees failed to add to their advantage in the second half and almost paid the price when Colchester were awarded a late penalty for Frank Onyeka's foul on Mandela Egbo.
An equaliser would have sent the tie to penalties, but Jack Payne's low effort was saved by goalkeeper Hakon Valdimarsson as Thomas Frank's team held on.
Toney's Future Uncertain
What's Next?
Brentford will host Leyton Orient in the third round of the Carabao Cup.