The Cobblers looked to be heading for victory at Spotland but Dale scored two late goals to edge a 3-2 win and go top of the Sky Bet League Two table.
Boothroyd's boys were in front just 40 seconds into the game when Luke Norris smashed home a glorious 25-yard strike.
The Cobblers proved difficult to break down in a frustrating second half for Dale - until Michael Rose sent an 88th-minute free-kick inside Matt Duke's near post and George Donnelly then netted the winner two minutes later.
"We have a very deflated dressing room after that," said Boothroyd. "It's all about very fine margins between winning and losing and for long periods you wouldn't have known which side was at the top of the league.
"But I said to the lads afterwards that the reason they are top of the league is because they keep going to the very end and we make silly mistakes.
"We conceded a silly free-kick, they score and the whole crowd is lifted and they get the momentum. The third goal was a poor one from our point of view.
"The game looked finished at 2-1 and it's difficult to take a defeat like that. But they are on a great run at the minute and things are going for them.
"We have to keep calm, show bloody-mindedness and keep going because I know that we will start winning games. There were many encouraging signs but they are difficult to see at the minute because we have lost."
- Sports & Recreation