Messi scored in the first half with a volley, before sealing a 2-0 victory for Barca with a penalty 10 minutes into the second period.
The Argentina international now has 100 goals for the Camp Nou club across the Champions League, Club World Cup and UEFA Super Cup.
400 - Lionel Messi has scored Barcelona's 400th goal under Luis Enrique (all competitions). Icon. pic.twitter.com/rSEtoy0NLl— OptaJose (@OptaJose) November 23, 2016
7 - Neymar has equalled the record for the most assists in a single Champions League season (since 2003-04). Giving.— OptaJoe (@OptaJoe) November 23, 2016
He has already scored nine in this season's Champions League, four clear of Edinson Cavani who sits second in the scoring charts.
The first goal was also Barca's 400th in all competitions under the management of Luis Enrique, while Neymar's assist meant he equalled the best tally in a Champions League season (seven) since 2003-04.