Roma and Lyon clinched their respective last-16 berths in the Europa League, while Athletic Bilbao were shocked by APOEL 2-0 to lose 4-3 on aggregate.
With a four-goal advantage going in to the return leg, Roma players slipped in their defence as Thomas Vermaelen's poor touch earned Rafael Borre a clear shot at goal from inside the box to break the deadlock in the 15th minute, reports Xinhua news agency.
However, the hole was too deep for the visitors to climb out. Roma finally made into the next round, while seeing their 16-game unbeaten home run shattered.
Contrary to Roma's lacklustre performance, Lyon, who led 4-1 in the first leg, geared up for another lopsided 7-1 win over AZ Alkmaar.
The other match between APOEL and Athletic Bilbao saw a goalless first half, before Pieros Sotiriou shot home on a left pass by Efrain just one minute into the second.
Giannis Giannotas scored for a confident APOEL on penalty after he was brought down inside the box in the 54th minute, surprisingly preventing the La Liga side from moving forward.
Tottenham Hotspur, currently ranked third in the Premier League, were also upset with an aggregate 3-2 loss to Gent of Belgium.
Ajax, Olympiacos and Besiktas also found their way ahead. Mourinho-led Manchester United eased through on an aggregate of 4-0 on Wednesday, along with Schalke and Russian outfit Krasnodar.