The hosts dominated for the entire evening and could have racked up a cricket score had they converted the possession and chances they created on home turf.
It was Gary Alexander's simple tap-in on 35 minutes that proved the difference after some brilliant work by Reading loanee James Henry down the Lions' right.
There was something close to a resurgence in the Cobblers midway through the second half once they shifted to a 4-4-2, but were simply not at the races in the opening 45 minutes.
Alexander, playing as a lone frontman, could have been in the clear four minutes in had he played to the whistle. He held his run onto Andy Frampton's incisive pass thinking he was offside, but the linesman waved him on once the chance had gone.
Midfielder Nadjim Abdou should have done better just before the half-hour mark when he air-kicked from just six yards out, after Marc Laird had squeezed the ball through to him.
Henry's persistence and a good advantage played by referee Grant Hegley created the Lions' opener. Henry skinned full-back Danny Jackman who pulled the winger down, but Henry raced back to his feet, got to the by-line and picked out Alexander who couldn't miss.
Henry almost added a second seven minutes after the break when his glancing header from Dave Martin's cross whistled past the post.
The remainder of the game petered out with little goalmouth action with the South Londoners having to cling on at times.
Lions keeper David Forde created a hairy moment 12 minutes from time when his poor punch fell to former Lions striker Leon Constantine, who tamely headed well wide.
Sub Liam Davis forced a late save from Forde with a fizzing low drive towards the bottom corner having darted off his left flank.