On 15 August 2016, Vidal scored the first goal of the 2016 DFL-Supercup match in a 2–0 victory over their fierce rival Borussia Dortmund.  He scored his first ever headed goal for Bayern in a 2–0 victory over Borussia Mönchengladbach on 22 October.  On 8 March 2017, he scored two goals in a 5–1 away victory over Arsenal in the Champions League round of sixteen second leg match.  On 12 April, he scored a header and also missed a penalty as his side suffered a 2–1 home defeat against Real Madrid in the Champions League semi-final first leg.  In the second leg, he was sent off for receiving a second yellow card after a controversial tackle on Marco Asensio and his side were again defeated and knocked out of the competition by Real Madrid with a 4–2 loss.  In the last game of the season, Vidal scored a goal in a 4–1 home victory over SC Freiburg and his side sealed a 25th win of the season and ensured they went a whole league campaign without a defeat at the Allianz Arena for the first time since 2008.