Sabiri, 22, sustained the injury three minutes after stepping off the bench in the midweek defeat at Bournemouth.
“Hamid unfortunately has broken his collarbone and will be out for eight weeks,” Wagner said.
“It’s very unlucky for Hamid. I really feel for him. He worked hard to get his opportunity and some minutes, but after a very short time he got this injury. We will give him all the support we can.”
The injury is a huge blow for the German Under-21 international, who has struggled to force his way into Wagner’s starting line-up since arriving from Nurnberg for an undisclosed fee in August.
He was making just his second Premier League appearance of the season at the Vitality Stadium after replacing Terence Kongolo in the 75th minute, but an awkward landing in a collision put paid to his bid for game time.
Sabiri could have been in contention for his first league start at Arsenal on Saturday as Philip Billing sits out a one-game ban after reaching five yellow cards.
Wagner confirmed fellow midfielders Danny Williams and Juninho Bacuna are in contention to start at the Emirates Stadium.
Striker Steve Mounie will serve the second game of his three-match ban following his red card in last Saturday’s home defeat to Brighton.
The Terriers will be boosted by the return to the squad of German left-back Chris Lowe, who was back in full training this week after missing three games due to his own shoulder injury.
Huddersfield dominated possession at Bournemouth and created more chances, but back-to-back defeats have left them one point above the bottom three.
Neither Mounie or fellow striker Laurent Depoitre have scored this season, but Wagner is careful not to add to the pressure they are both under.
“I will still be patient,” Wagner said. “Anything else makes no sense, even if we know we need goals from them, as we do from other positions as well.”
The Terriers were thrashed 5-0 at the Emirates last season - they lost 1-0 at home on the final day - and Wagner is keen for his side to show they are better than the scoreline suggests.
“I hope and I think we learned our lessons from our first game at the Emirates,” he added. “Now we have to show we have progressed and improved. It’s as simple as that.”