First-half substitute Rajiv Van la Parra struck first and Danny Williams added the second within a minute, although his speculative effort took a big deflection.
Derik Osede gave the hosts hope by heading home from a corner in the 63rd minute but they failed to force an equaliser in this Roses duel watched by almost 4,000 Town fans.
New signing Terence Kongolo made his debut and was one of eight changes from Town’s last Premier League game.
The Dutch international signed on loan from Monaco played in the heart of the defence alongside Michael Hefele, who is making his comeback from an Achilles operation.
Bolton, who have just pulled out of the Championship’s relegation zone, also showed seven changes, injuries and loan recalls having decimated their midfield.
There were starting berths for former Rotherham striker Adam Le Fondre, ex Bradford star Filipe Morais and former Sheffield United goalkeeper Mark Howard.
In a quiet opening quarter, Josh Vela was booked for a late challenge on Town’s Danny Williams.
Hefele was booked for a foul on Le Fondre, Collin Quaner hobbled off before the break to be replaced by Van la Parra and Bolton striker Aaron Wilbraham wasted the only good chance of the half, heading wide from seven yards.
Town soon took the lead after the break. Abdel Sabiri’s fierce shot set up the first of four successive corners and Van la Parra forced the latter home from close range. Almost immediately, Danny Williams let fly from the centre of the field and the ball took a big deflection off Wheater to leave Howard flat-footed as Town took a 2-0 lead in the 52nd minute.
Bolton finally pressed and unmarked Osede headed home from their first corner 11 minutes later.
In response, Williams let fly again and Howard tipped over his effort before Osede’s snap-shot went narrowly over at the other end.
Howard again denied Williams as Town broke late on before goalkeeper Joel Coleman was booked for time-wasting.
Rival managers David Wagner and Phil Parkinson were at odds over a “leg-breaker” challenge leading up to Huddersfield’s second goal.
Bolton boss Phil Parkinson felt his defender David Wheater could have sustained serious injury when tackled by Huddersfield midfielder Abdelhamid Sabiri in the build-up to Huddersfield’s second goal.
“You’ve got to see the challenge on David Wheater in the middle of the park to believe it,” Parkinson said.
“It’s a leg-breaking challenge right in front of the referee and he hasn’t given it and it’s resulted in the lad having a shot and a deflected goal.
“Really that goal should never have stood and I thought we reacted well after that, got back in the game and looked the most likely to get a draw and take it to a replay.”
Roger East had let play continue but Parkinson indicated he would speak to the referee about the incident.
“The tackle on Wheater, I’ve just seen it again,” Parkinson added. “The lad’s gone right over the top of the ball. The state of Wheater’s leg, he’s very lucky not to have a serious injury.
“I’m going to ask the ref in a minute how he hasn’t seen that incident because it’s right in front of him and it’s the type of challenge which can result in serious injury.
“Today, not only that, it’s resulted in a goal, which has probably cost us at least getting a replay.”
Wagner, delighted with his side’s display after making eight changes, felt Sabiri was fouled prior to his challenge on Wheater.
“From my point of view it was a foul on Sabiri, a clear holding and then he tried to get the ball with a long leg,” said the German.
“It could be that afterwards there was a tackle, but I was surprised we didn’t get a foul in this situation because of the holding on Sabiri.
“Then came this challenge and the ball ended at Danny Williams’ feet and he scored, so if we have to speak about the challenge then we have to speak about the situation half a second before when it was a foul on Sabiri.”
“We looked very focused and never rushed the situation. I was, even in the first half, satisfied that we looked so professional,” Wagner added.
“Everybody knows how difficult it can be if you play in the cup against an opponent in a league below you and I never had the feeling we were really in trouble.”
Verdict: With league survival the priority for both sides in their respective divisions, it was no surprise that there were wholesale changes and the tie did not come alive until after the break.