Alex Nicholls grabbed a late winner to earn the Cobblers all three points.
"Our performance in the first 35 minutes was as good as any we've produced since I've been here," enthused Boothroyd.
"I thought we were well worth our win. We were fantastic, the work ethic, commitment and our passing was excellent, and we outplayed them in the middle of the park.
"The only thing I was disappointed about was that we didn't score three or four goals because we created some great chances.
"But Rotherham are a very good side and I knew they would come back at us. They were stronger than us for long periods in the second half but if teams want to try and dominate us we've got quick players who can catch them on the break."