Diego Costa and Kevin Gameiro scored second-half goals to give Atletico a 2-0 win over Athletic Bilbao and keep it seven points behind Barcelona at the top of the table.
Arsenal powered past Ostersund 3-0, Atletico Madrid thrashed Copenhagen 4-1 and Italian league leader Napoli slipped to a surprise 3-1 home defeat against Leipzig.
Ronaldo's treble of goals on Saturday fueled a 5-2 victory at home over a disconcerted Real Sociedad, which barely offered resistance in a first half dominated by Madrid.
Luciano Vietto scored three times — including one from near midfield — to help Valencia rout Las Palmas 4-0 and advance 5-1 on aggregate.
The Madrid's officials have filed a complaint over an illegal approach to bring the striker to the Catalan club.
With Atletico being knocked out of the Champions League and now in the Europa League, the Frenchman now sets his eyes on a move but where is an unanswered question.
The 33-year-old knows his place is under threat when Diego Costa and Vitolo are included in the squad from January onwards.
Madrid, twice a finalist in the last four years and a semifinalist last season, will instead be back in the Europa League for the first time since the 2012-13 season.
Barcelona striker Paco Alcacer scored in the first half and Gerard Pique, Aleix Vidal, Denis Suarez and Jose Arnaiz each added goals after halftime to give the hosts an 8-0 aggregate win against the third-tier club.
With six points in Group C, Atletico trail Roma by two points and is four points behind Chelsea, which had secured its spot in the last 16 by beating Qarabag 4-0 in Azerbaijan.
The Madrid rivals played to a scoreless draw at Atletico's new venue on Saturday, leaving both teams further away from the Catalan club at the top of the Spanish league.
After being held by 10-man Qarabag to a 1-1 draw in Group C on Tuesday, Atletico are still winless after four matches.
Messi again showcased his multi skillset with a dazzling display of playmaking and finishing while leading Barcelona to another win.
The much-needed victory came for Atletico after back to back draws in the league along with a loss to Chelsea and a draw at Qarabag in the UCL.
With just two points from three matches in the UCL so far, Diego Simeone's men face a real possibility of an early exit.
The result ended Barcelona's perfect league record and cut the club's lead to five points over Real Madrid, which defeated Getafe 2-1 with a late winner by Cristiano Ronaldo.
The Argentine coach praised Barcelona's star Lionel Messi, who scored 27 goals in 34 matches between both sides in all competitions.
Alvaro Morata had added to his impressive start with Chelsea by scoring a second-half equalizer after Atletico had taken the lead before halftime with a penalty converted by Antoine Griezmann.
After both sides had hit the woodwork, Carrasco opened the scoring two minutes after halftime and Griezmann sealed the victory in the 70th.
The Brazilian-born Spaniard acknowledged that he grew "a little nervous" as time passed without an agreement between Chelsea and Atletico Madrid.
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