Goals from John Johnson and Akwasi Asante did the damage at Morecambe with the Shrimps causing some late panic for the Cobblers thanks to Ellison's strike.
That proved to be a consolation only though as the visitors took all three points to close the gap on the teams above them in the League Two relegation battle.
Boothroyd will have been delighted at the performances of his new signings and especially the problems caused by young strike duo Asante and Berahino.
"Morecambe are a very good side but we dug in and held them out and managed to score from a set piece and a counter attack and our game plan worked really well," said the Town boss.
"It's been a long time coming and I am delighted for the players and the fans and I think we deserved it overall.
"It's a big relief for everyone but I know it has been coming and hopefully we can now go on and build on it."