Town now lie 14th in League Two after continuing their solid Sixfields form, John Johnson netting a late winner to see off the Imps.
Northampton are at home again next Saturday when they entertain Cheltenham.
"The league table is very tight and we just need to find a bit of consistency," Ian Sampson told the club website afterwards.
"That's three wins from our last four games now and if we can get three wins from our next four games then I'm sure we will be on the edge of the play-offs."
Sampson is also confident that Ben Tozer will be able to extend his loan deal with the club, praising the defender's display against Lincoln.