A romp for the new league leaders looking at the scoreline was far from it as they had to come from behind twice against a Northampton side who showed no fear against their lofty opponents.
Johnson and Berahino scored for the hosts in front of 5,255 at Sixfields and the game was all square going into the final ten minutes.
The quality that means Southend are gunning for League One football next season then showed to give them the three points and put an unfair gloss on the result and leave Boothroyd's side once again at the foot of the Football League.
He told BBC Radio Northampton afterwards: "For me, I wouldn't have been able to tell which team was at the top and which was at the bottom, for long periods.
"I think the clearest thing is that they bring a player on who scores two goals for them. We didn't switch on in the latter stages of the game.
"Was it a 5-2 game in terms of performance? Absolutely not. But we never give up. We're going to need that every week."