Although Chelsea failed to keep a perfect group-stage record, Willian and Giroud salvaged a 2-2 draw against Vidi in Budapest by scoring from free kicks.
Sevilla, which has eclipsed Barcelona and Real Madrid so far this season to lead the way in the Spanish league, suffered a surprise 1-0 loss at Standard Liege in Group J.
It was Ronaldo's first goal in six matches at San Siro, having previously played at the iconic stadium for Manchester United and Real Madrid.
AC Milan suffered a shock 2-1 defeat against Real Betis at the San Siro, while Arsenal was unstoppable again as it remained perfect in the competition.
Inter star player Nainggolan hurt his ankle in a crunching tackle with Lucas Biglia in the first half. The Belgian midfielder will undergo tests on Monday but is now a doubt for Champions League match at Barcelona.
Arsenal, with former Sevilla coach Unai Emery now in charge, defeated Ukraine's Vorskla 4-2 thanks to a double from Pierre-Emerick Aubameyang and AC Milan edged past Dudelange of Luxembourg 1-0.
Juventus said in a statement that Bonucci and Caldara are direct swaps with each player being valued at 35 million euros ($41 million).
Wilkins had an illustrious career with Manchester United, Chelsea and AC Milan and had coached QPR and Fulham as well.
Marseille progressed after a 2-1 win at Athletic Bilbao that was marred by crowd trouble. Lazio advanced with a 2-0 win at Dinamo Kiev and Leipzig drew 1-1 at Zenit.
There was another surprise in Germany where two goals from Valon Berisha led Salzburg to a 2-1 victory at Borussia Dortmund.
Juventus was also slated to host Atalanta in Serie A on Sunday but that match was snowed out and will be made up March 14.
Athletic Bilbao are scheduled to next face Marseille, while Borussia Dortmund will take on Austrian side Salzburg.
Shockingly, Serie A leaders Napoli weren't good enough to advance in the Europa League on Thursday after they were knocked out in Germany by RP Leipzig.
In other ties, Scottish club Celtic F.C will host Russian club Zenit St Petersburg, Napoli will play RB Leipzig, Ludogorets will take on seven-time European champions AC Milan.
Unable to produce inspiring results with a completely revamped squad, Montella was fired as coach of AC Milan and replaced by Gennaro Gattuso.
Lyon routed Apollon 4-0 and Atalanta hammered Everton 5-1 in Goodison Park, leaving the Premier League side winless, to confirm their dominance in Group E.
The former Manchester City player who along with a group of five other men have been found guilty of sexually assaulting an Albanian girl in a Milan club in January, 2013.
Undefeated Inter took sole possession of second place, moving two points behind perfect Napoli and three ahead of six-time defending champion Juventus and Lazio.
Milan returns to UEFA competitions after a three-year absence and avoided long travel for Thursday games that lurk in the 48-team draw.
The 44-year-old owes his ex-partner Barbara Thurler 61,000 reais (around $20,000) of child support.
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