The 20-year-old is out-of-contract at Sixfields this summer and had rejected a new deal, although Derby's previous offers of compensation had fallen well short of Town's valuation, making a tribunal likely.
But the two clubs have finally agreed on a fee, which is required due to Jacobs being under 24 years of age, and the promising wide man has agreed a three-year deal at Pride Park to become County's first summer signing.
Rams boss Nigel Clough beat off top-flight competition to land Jacobs and is delighted to secure who he believes over the last two years has been "one of the best players in the lower leagues".
Clough added on Derby's official website: "He's a young lad but already he has plenty of first-team experience at Northampton behind him and we feel he has plenty of potential, which we believe he can fulfil in a Derby County shirt.
"Michael fits in well with the sort of player we're looking to bring into the club and we're delighted he's chosen Derby County after hearing what we've had to say and having a look around. We've had to be patient in getting this deal done, but we're very happy to get it over the line."