Geoffrey Kondogbia’s deflected 25-yard strike gave Monaco the lead seven minutes before half-time in north London.
Today probably we wanted the win more than them
Former Tottenham Hotspur striker Berbatov then finished off a counter-attack from 12 yards to make it 2-0 in the 53rd minute.
Arsenal pulled a goal back when substitute Alex Oxlade-Chamberlain curled home in the 90th minute.
But Yannick Ferreira Carrasco scored in stoppage time to put Monaco in charge of the last-16 tie ahead of the second leg on 17 March.
Speaking to Sky Sports after the game, Berbatov claimed that the Gunners were guilty of underestimating their opposition.
“We are confident in our ability so honestly we deserved to win,” said Berbatov.
“We scored our chances and in the end it’s a great win for us. It’s not over, we have one more game in Monaco and Arsenal are a great team.
“We are good. Arsenal is a good team but today probably we wanted the win more than them, We fought all over the pitch, won our challenges and scored the goals.”
The Gunners will need to score at least three goals in Monaco to have any hope of progressing to the quarter-finals.
Arsenal’s next game is a home clash with Everton in the Premier League on Sunday afternoon.
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