Both games were scintillating contests especially the thriller in Lithuania where Real fought back from a 14-point third-quarter deficit to improve their record to 9-1 in the second group stage of the competition and close in on a playoff berth.
Their joy was cut short however when Zalgiris fans assaulted Fernandez as the players were boarding the team bus, prompting an investigation by Euroleague's disciplinary committee.
"Two people tried to attack the player and the security person the club had allocated to him," Real's basketball section director Juan Carlos Sanchez Lazaro told the club's website (www.realmadrid.com).
"(Fernandez) suffered a blow to the neck and the shoulder but the security person came off worse. He received several blows before the police, who were outside, could get in to restrain the individuals.
"The player is OK but he is a bit scared because what happened was a disgrace and something that nobody from any sport wants."
The incident marred a rip-roaring encounter that swung Real's way after they also overcame a seven-point deficit in the final minute of regular time and edged out the hosts with a barrage of three-pointers in overtime.
Montenegrin-born forward Nikola Mirotic shone for the winners with a game-high 31 points after hitting all 18 shots from the foul line. American guard Jaycee Carroll poured in 21 including five three-pointers from seven attempts.
Eight-times champions Real are top of their eight-team pool and need one win from their remaining four games to reach the best-of-five quarter-final playoff series.
The winners from that series advance to the May 10-12 Final Four at London's O2 Arena.
Barcelona, who top the other pool, also claimed their ninth win in 10 games to seal their passage into the last eight after Slovenian forward Erazem Lorbek buried 21 points, hitting seven of eight shots from two-point range.
Roared on by noisy fans in the Peace and Friendship Stadium, Olympiacos held their own for three quarters but were blown away by the 2010 champions in the final period.
"Barcelona are the best team in the Euroleague and tonight they showed their class and quality," said Olympiacos guard Kostas Sloukas.
Barca coach Xavi Pasqual said: "We thank the Greek fans of Barcelona who came here and gave us big support. It was a great game between two very good teams."
Second-placed Montepaschi Siena have a 7-3 record after their 78-71 reverse at Khimki Moscow who are joint third with Olympiacos on six wins and four defeats.
Turkish teams in that group had little to cheer as quadruple champions Maccabi Tel Aviv strolled to a 94-85 win at Fenerbahce and Spaniards Caja Laboral Vitoria triumphed 83-73 at Besiktas.
Maccabi and Caja kept alive their hopes of breaking into the top four. They have five wins and as many defeats but Istanbul rivals Fenerbahce (2-8) and Besiktas (0-10) are out of the reckoning.
Anadolu Efes Istanbul (8-2) are second in Real's pool after winning 91-86 at Alba Berlin thanks to 23 points from former Los Angeles Lakers guard Jordan Farmar.
Third-placed CSKA Moscow (7-3) breezed past Germany's Bamberg 78-58.
Six-times champions Panathinaikos Athens (6-4) are fourth with Unicaja Malaga (5-5) breathing down their necks after the Spanish team conjured an 11-0 run in a furious finish to beat the Greek side 66-60 with 22 points coming from guard Marcus Williams.