Shaun Harrad's penalty cancelled out an earlier spot kick for the home side and ensured that Gary Johnson was not on the losing side for the first time as Northampton boss.
With Barnet losing there are now seven points between Town and the final relegation place.
Johnson told the official club website afterwards that his players had shown a 'winning mentality' after going behind.
"With a little bit more quality in front of goal we could have taken all three points," he said.