Jabo Ibehre struck a second-half double to inflict a sixth successive defeat on Stevenage and boost Colchester's hopes of avoiding relegation from League One.
The 30-year-old attacker struck for the first time in seven games to give Colchester the lead on 62 minutes with a fine header.
And Ibehre secured a 2-0 win for the visitors when he tapped in after a fine run from Gavin Massey to lift Colchester out of the relegation zone.
George Porter almost opened the scoring for the U's by beating a diving Chris Day but his 31st-minute effort was hacked off the line by right-back David Gray.
Gray's clearance found Ibehre unmarked in the area but the Boro keeper recovered to force the effort wide.
Moments later Anthony Grant almost gave the hosts the lead but Sam Walker instinctively pushed the ball wide.
But Ibehre towered above the Boro defence to drive a header into the top-right corner of Day's goal from Billy Clifford's free-kick.
Ibehre doubled the lead with a tap-in before Marcus Haber almost gave Boro hope but fired into the side netting after beating several U's defenders.