Midfielder Flynn, signed from Gillingham in the summer, missed two good first-chance chances but made up for it after the break.
Flynn has had a tough start to his Huddersfield career, missing chances galore but it all came right against fellow strugglers Northampton.
The Cobblers, without an away win since March, had a couple of early chances through striker Karl Hawley, one of which was cleared off the line by Nathan Clarke.
Flynn just failed to connect with Andy Booth's header at the back post and then Clarke was denied by Adebayo Akinfenwa's stooping header off the line.
A flying header from Flynn would have made a spectacular opener as Huddersfield dominated.
However, the home side went behind when Daniel Jackman fed Luke Guttridge out wide. His attempted cross deflected off Jim Goodwin and looped over keeper Matt Glennon.
Colin Larkin scraped the outside of the post as the Cobblers almost made Huddersfield pay for missing chances.
Flynn and Liam Dickinson, though, combined to set up Booth's equaliser, the veteran striker scoring from close range after a loose ball had broken kindly for him.
Flynn, who also screwed a shot wide in first-half stoppage time, put Huddersfield in front in the 64th minute when he planted his finish from Dickinson's cross into the bottom corner.
Huddersfield took control after that but it took a lucky break to make the points safe.
Flynn grabbed his second 12 minutes from time when his 20-yard shot squirmed through the hands of keeper Chris Dunn and bobbled over the line.
The Cobblers made Huddersfield sweat late on when sub Liam Davis headed home in stoppage time.