A carnival atmosphere before kick-off quickly turned sour for more than 11,000 Vale fans when Northampton took a third minute lead through Clarke Carlisle.
Liam Chilvers equalised but a sublime 20-yard finish by Roy O'Donovan, who curled the ball high inside Chris Neal's right-hand post from Hornby's pass in the 69th minute, looked to have won it until Lee Collins' late gaffe earned Vale promotion.
With his side set to prepare for the play-offs after hosting Barnet next Saturday, Boothroyd said: "I picked a team which I thought would cause Vale problems and we certainly did. Young David Moyo is exceptionally quick and I thought his pace could get at the centre of Vale's defence.
"If it wasn't for a freak own goal we would have won, but Lee Collins was brilliant out there and we are all disappointed for him.
"Last season this club only got 46 points so to reach the 70-point mark with a game to go is a magnificent achievement by all concerned.
"We've got the Barnet game to take care of and we will be doing our best to win that one and take some momentum into the play-offs.
" There are certainly plenty of positives to take from this game, but congratulations to Port Vale. They have been up there near the top of the league all season and deserve to be promoted."