Mathias Pogba hit the second-half winner as Crewe dented Colchester United's League One survival hopes.
Luke Murphy gave the Railwaymen the lead from the spot after Josh Thompson handled Gregor Robertson's cross.
U's defender Magnus Okuonghae then had a header cleared off the line before George Porter slotted home to level for the hosts by half-time after good work from substitute Michael Smith.
However, Murphy found Pogba in the area to hit his 14th goal of the season.
New Crewe signing Nathan Ellington remained on the bench as top scorer Pogba's 72nd-minute strike ended the Alex's untimely run of four defeats in five games, to edge them back within 11 points of the play-offs.
With Jabo Ibehre starting a three-game ban and fellow striker Freddie Sears (knee) also absent, Colchester gave debuts to their two midweek loan signings, Troy Hewitt (QPR) and Michael Smith (Charlton Athletic), who both came off the bench.