South Korean striker Dong Gook Lee finally grabbed his first Middlesbrough goal as the 2004 winners rode their luck to book their place in the Carling Cup third round.
Lee drove home a powerful low shot from the edge of the box in the 66th minute to wrap up victory for Gareth Southgate's men after Fabio Rochemback's free-kick had broken the deadlock.
But it could have been a different story for spluttering Boro had the bright Coca-Cola League One outfit capitalised on early chances, the best of which saw Ian Henderson's diving header hit the post.
Lee, who had failed to hit the net in his handful of appearances since joining Boro in January, was one of six new faces introduced by Southgate after Sunday's draw with Newcastle.
He might have made life a whole lot easier for his side had he aimed a fifth minute header on target after connecting with Luke Young's deep cross from the right.
Instead Northampton almost surged into a shock lead. Three minutes later Brad Johnson's drive was parried by Boro keeper Brad Jones into the path of Henderson, who clattered the woodwork.
Adam Johnson brought a fine save out of Mark Bunn in the Cobblers' goal and Mark Hughes hacked clear a dangerous Rochemback free-kick as Boro seemed to wrest control.
But with Lee and Tuncay Sanli looking increasingly ineffective up front, Northampton clearly fancied their chances and came close again on the half hour.
Their 17-year-old debutant Alex Dyer almost made a dream start when he skipped around Young in the Boro box before driving a low shot which Jones did well to parry.
Finally the frustration in the sparsely populated stands was lifted in the 53rd minute when Rochemback fired home a low free-kick from 35 yards after Johnson's foul on Lee.
They almost increased their lead in the 65th minute when Lee's header from a Rochemback corner was saved at point-blank range and substitute Seb Hines' overhead kick hit the bar.
But Lee took his chance in the 66th minute when he was played in by Stewart Downing and produced a clinical finish to finally get his Boro career up and running.
The League One side kept pushing and ought to have narrowed the deficit in the 71st minute when Henderson's close-range shot was booted off the line by Young.
But Boro should have had a third in the 76th minute when substitute Mido headed an Adam Johnson cross from the right against the bar from close range.
And the impressive Egyptian - clearly looking to build on his fine start to his Boro career - also brought a good low save out of Bunn in the dying minutes.
