Alex Nicholls hit the second-half winner as Cobblers overcame the setback of falling behind to beat the Bluebirds 2-1 in the first round.
Heidar Helguson gave City the early lead but goals either side of the break from David Artell and Nicholls were enough for Northampton to claim another big scalp in the competition.
"I don't want to get too carried away but I'm really excited about the players we've got here and what we might be able to do this season," said Boothroyd.
"The win at Liverpool a couple of seasons ago under Ian Sampson was one of the great results in this competition in recent years.
"But a lot of teams in League One and Two go on good cup runs each season but their league form suffers. It's important we celebrate tonight's result but then focus on the next league game and not get too carried away.
"Sometimes players get carried away with a cup win like this and then don't focus on the league. I don't want to be a team that has a good cup run and knocks a big team out of the cup but finishes near the bottom of the table."
Cardiff boss Malky Mackay was philosophical following the defeat. Mackay was missing key players through the midweek internationals and injuries.
"We knew it would be a tough game at Northampton and an even tougher one with the international call-ups and having to play on Friday," said the Cardiff boss.
"It's great for the club to have international players but you just hope they come back without any injuries.
"We want to win every game we play but if it wasn't us going through tonight then I'm glad it's Aidy Boothroyd's side."
Despite the defeat, Mackay was delighted to see new signing Helguson get off the mark on his debut.
"We know Heidar Helguson can score goals and that's why we brought him in but he needs more time on the pitch.
"We still need to bring in a few more players before the transfer deadline. It's important to get off to a good start against Huddersfield on Friday and that's what we must look forward to now."