Twins Nauris and Normunds Macius, known in Lithuania as leaders of the die-hard Zalgiris supporters, punched Fernandez after Real's 105-104 overtime win at the Lithuanian champions last Thursday when the visitors were boarding the team bus.
"We will have zero tolerance for violence in Euroleague arenas," the competition's ruling body Euroleague Basketball said. It also fined Zalgiris 25,000 euros for the incident.
Zalgiris have also lost forward Tremmel Darden, who joined Real on Wednesday but is ineligible to play for the eight-time winners of Europe's premier club basketball competition until next season.
The defeat at six-time winners CSKA left Zalgiris with no chance of reaching the best-of-five quarter-final play-off series even though they still have three games to play in the top 16, the second group stage featuring two pools of eight teams.
CSKA improved to 8-3 and edged closer to the play-offs, whose winners will advance to the May 10-12 Final Four in London.
"We had 16 turnovers and missed a number of easy shots but I think we made our fans proud by giving a huge effort," Zalgiris coach Joan Plaza told the competition's website.
His CSKA counterpart Ettore Messina added: "This game became mentally difficult before it even started; we were supposed to win for sure after Darden left and (Zalgiris guard) Marko Popovic got injured but we switched off after building a 15-point lead."
Zalgiris briefly hauled themselves back into the match in the second half but were unable to hold off CSKA in the fourth quarter, as forward Sonny Weems led the winners with 13 points against his former club.
CSKA stayed third in their pool, behind Real and Anadolu Efes Istanbul who have nine wins and two defeats each.
Real missed the chance to secure a play-off berth with a 77-74 home loss to compatriots Unicaja Malaga, whose Croatian duo Luka Zoric and Krunoslav Simon got 39 points between them.
Efes earned an 89-86 overtime home success against winless German side Bamberg with a superb display by former Los Angeles Lakers guard Jordan Farmar, the game's top scorer on 29 points.
Six-time Euroleague winners Panathinaikos Athens (7-4) strolled to an 82-58 rout of Alba Berlin and remain ahead of Unicaja who stay fifth with six wins and five defeats.
Barcelona, 86-61 winners over Besiktas, claimed a place in the quarter-finals from the other pool last week but the race for the other three spots is set to be a thrilling battle as five teams have an even chance of joining the 2010 champions.
Holders Olympiakos Piraeus took a big step towards the last eight with a 68-67 win at Italians Montepaschi Siena and the result left both teams on seven wins and four defeats.
They are followed by Khimki Moscow, former quadruple winners Maccabi Tel Aviv and Spaniards Caja Laboral Vitoria, who all have 6-5 records.
Forward Ricky Hickman poured 30 points in Maccabi's frantic 80-79 home win over Khimki, with the lead changing hands time and again in the roller coaster played in a raucous atmosphere.
Hickman nailed several three-pointers at crunch time and swung the match Maccabi's way with an audacious slam-dunk after weaving his way past Khimki's Croatian playmaker Zoran Planinic.
"I said the players needed to die on the court, symbolically," said Maccabi coach David Blatt, who steered Russia to the 2007 European Championship title in Spain.
"I said we weren't out of the race after some painful defeats in the first half of the top 16, now after winning five of the last six games I say we're not there yet because we are still very far."
Caja Laboral, who are also having a topsy-turvy season, kept alive their hopes with an 87-67 home win over Fenerbahce Istanbul after five of their players finished in double scoring digits.
German centre Tibor Pleiss led the charge with 14 points, netting seven of eight shots from the field. Former Chicago Bulls guard Andres Nocioni, Maciej Lampe and Fabien Causeur added 12 each while Thomas Heurtel chipped in with 11.
"It was a tough game because we had everything to fight for and they had nothing to lose," Caja's Croatian coach Zan Tabak said.
"It's all in our hands now, we have three games against strong opponents but we can qualify without other results going our way."