Arsenal's path to the final was more straightforward, beating Valencia 4-2 thanks to a hat trick from Pierre-Emerick Aubameyang to complete a 7-3 win on aggregate.
Arsenal will take a 3-1 lead into the second leg against Valencia after coming from behind while Chelsea scored the potentially crucial away goal in Germany to extend his team's unbeaten run.
Since back-to-back wins over Napoli, the second best team in Italy, in the quarterfinals of the Europa League, Arsenal's players have lost three straight games in the Premier League.
Chelsea beat Slavia Prague 4-3 on aggregate over the two legs while Arsenal got the better of Napoli 3-0 to make the Europa League last four for the second straight year.
In other Europa League games, Benfica beat Eintracht Frankfurt 4-2 after Joao Felix's hat trick while Valencia secured a 3-1 away win at Villarreal.
With Napoli in a comfortable second place in Serie A, Ancelotti looks sure to lead the team back into the Champions League next season.
There were two upsets, though, as five-time champion Sevilla and Inter Milan were both eliminated.
Arsenal took the lead through Iwobi after just four minutes but the game turned when Sokratis was sent off, resulting in Rennes going all out and netting in three goals.
Valencia went through 3-0 on aggregate after beating Celtic 1-0 at home.
Arsenal dominated possession but was stunned just before the break when Stanislav Dragun got his head to Borisov captain Igor Stasevich's dangerous free kick.
The violence erupted around 9.30 p.m. on Wednesday near the Coliseum where four people - two Spaniards, an American and a Briton - were shot, reports Efe news.
Napoli and Inter Milan will only have to cross the Italian border into neighboring countries for games against Zurich and Rapid Vienna, respectively.
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.
Giroud had not scored for Chelsea for six months but he knows what it's like to net against BATE.
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.
Spain forward Morata scored his first goal for Sarri's blues since August, and only his second of the season to help Chelsea edge Vidi in the group stage match.
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.
Atletico Madrid players paraded through the Spanish capital on Friday to celebrate the team's Europa League triumph.
Rafael Nadal appeared with a Atletico Madrid jersey during the club's Europa League match against Arsenal last week.
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