The Polish sharpshooter was once more Die Roten's saviour as he swooped in the 96th minute to ensure his team would not leave Berlin empty-handed.
The Argentine netted an eye-catching brace, with his countryman Gonzalo Higuain and Claudio Marchisio also on target for the Serie A leaders.
The striker continued his fine run of form in front of goal as Jose Mourinho's men secured victory in the Europa League at Old Trafford.
Arjen Robben, Robert Lewandowski, Thiago Alcantara and Thomas Muller scored the goals to leave the Gunners facing yet another last 16 exit.
The 29-year-old struck either side of half-time as the Old Lady triumph on Massimiliano Allegri's 100th Serie A game in charge.
A devastating second-half spell yielded four goals in just eight minutes for the defending Liga champions, who were beaten at Camp Nou by the Basques.
Two goals in the last five minutes of the first half propelled the Red Devils three points and have plunged the champions into even greater trouble. Manchester United gave their top-four aspirations a major boost as they cruised to a 3-0 win at Premier League champions Leicester City on Sunday.