This was still a very young Southend team as first teamers such as Walker and Freedman were kept back but Osei Sankofa played 90 minutes at right back for the first time in several weeks, along with regular bench warmer Stuart O'Keefe.
Rochdale trailist Scott Spencer placed the ball in the net as early as the 18th minute to give Southend the lead after the referee waved played on after Justin Clayton had been fouled on the edge of the penalty area.
In fact Spencer was involved in most of the early exchanges and again just before the interval, he must have done his chances of at least another game no harm at all.
The returning Sankofa smacked a low shot into the hands of the Col U keeper Shane Cusack who then saw his side get a surprise equaliser on the half hour.
A great run into the box by Craig Arnott found Jordan Pavett who smashed the ball past Ian Joyce.
Blues Two's retook the lead four minutes before half-time when Craig Calver passed for Stuart O'Keefe to hit home.
A more even game in the second period and it was the reserve Farmers who equalised for the second time two minutes after the hour mark, Michael Rafter crossing from wide right where Craig Arnott found himself unmarked and able to ease the ball home.
So a derby draw seemed to be the favoured result at this stage, until Spencer decided he would not be denied, and on 80 minutes after Colchester failed to clear a free-kick floated into their area, he struck the ball off the right hand post into the net for the winner.
Still time for a strong Shrimpers penalty appeal to be turned down when Harry Crawford was brought down, and at the other end for Pavett to escape the tight marking of Duran Reynolds to lob Joyce as he came out of his goal, but the ball fell inches wide.
With the under-18's also beating the team from the other end of Essex earlier this season, it's up to the seniors on Boxing Day to make it a very welcome victory hat-trick!
Southend United: Joyce, Sankofa, Wilson, James-Lewis (Dennis 74), Clayton, Milner, O'Keefe, Calver, Spencer, Asante (Crawford 81).