The Gunners were able to keep Europe’s most-prolific side at bay for 71 minutes before Lionel Messi completed a brilliant counter-attacking move, which involved Neymar and Luis Suarez.
Arsene Wenger brought on Mathieu Flamini for Francis Coquelin with seven minutes remaining to add fresh legs to his waning Arsenal side at the Emirates Stadium.
However, the French midfielder brought down Messi in the penalty area and the Argentina international dispatched his penalty to secure a 2-0 victory in the first leg of the last-16 tie.
Arsenal travel to the Camp Nou on 16 March in search of a memorable comeback as the north London side look to reach the Champions League quarter-finals for the first time since 2010.
Outspoken supporters Morgan was critical of Wenger’s poor recent record in the Champions League on Twitter following Tuesday night’s defeat.
Wenger's 'brilliant' CL record continues: 6 consecutive years going out at L16 stage.
— Piers Morgan (@piersmorgan) February 23, 2016
Arsenal make the trip to Manchester United in the Premier League on Sunday.
MORE: Latest Man Utd news
MORE: Latest Arsenal news
MORE: The latest football news