The U23s' unbeaten run came to an end on a windy afternoon in Suffolk.
With a much-changed side from the one that had beaten West Bromwich Albion to advance in the Premier League Cup last time out, the Clarets gave a first start at this level to striker Lewis Richardson.
And there was also a debut from the bench for Under-16 team-mate Ben Woods against a stronger and much more experienced Ipswich side who included first-team players Kayden Jackson, Andre Dozzell and Josh Emmanuel and held off a spirited Clarets' performance to bank the points with two first-half goals.
With the weather conditions playing a huge part in the opening 20 minutes and both teams having to adjust to Storm Freya, it was the Clarets who had the first real chance.
Seventeen-year-old Mitch George fizzed the ball across the face of goal for Richardson, who was lurking at the back post but narrowly missed the ball as it rolled out of play.
Mitch George went close for the Clarets
And minutes later Ipswich had their opener as Jackson broke into the box before teeing up El Minouzi, who slotted home from close range past a stranded Aiden Stone.
The hosts - leaders of the Professional Development League's southern group - had their second five minutes later as Joe Cotter back-heeled a loose ball into the net following a free-kick and goal-mouth scramble.
But the Clarets still looked bright and came close to pulling one back with Richardson striking the bar from a few yards out.
The break saw boss Steve Stone introduce 16-year old Woods and 18-year old Will Harris, and the young pair played a part in a much-improved second half from the visitors.
Burnley were inches away from snatching a goal with 20 minutes to play, as a Harris strike was parried into the path of Tinashe Chakwana, whose effort from a couple of yards out was excellently kept out by Harry Wright.
And Stone’s side then hit the bar for a second time, as George’s free-kick rattled off the frame of the goal before being cleared with the clock ticking.
Despite the Clarets’ best efforts at clawing something from the game, the young side fell to their first defeat since the first week of January to end an an eight-match unbeaten run and stay third in the northern section.
Burnley: Stone, Clarke, Cropper, Perkins, Wilson, Chakwana (Agyei 62), Trialist, George, N’Guessan (Woods HT), Harker (Harris HT), Richardson.
Ipswich: Wright, Emmanuel, Cotter, Ndaba (C), Webber, McGavin, Dozzell, Dobra, Dawkins, El Mizouni, Jackson.