Romelu Lukaku hit the bar while the game was goalless, when it appeared easier to score, and Brazilian midfielder Fred struck a post for United.
Arsenal keeper Bernd Leno also produced two crucial saves to keep out Lukaku, before Pierre-Emerick Aubameyang doubled the hosts’ lead from the penalty spot after Fred’s foul on Alexandre Lacazette.
Soon after Arsenal’s second goal, a fan ran on to the pitch and shoved United defender Chris Smalling before being removed by stewards
The Gunners have won seven out of 10 top-flight games in 2019 and are one point behind north London rivals Tottenham, who sit third in the table, with eight games remaining.
United, who started the weekend in fourth, drop to fifth in the race for a Champions League spot next season.
“Tottenham Hotspur, we’re coming for you” chants filled Emirates Stadium at the final whistle as Arsenal fans celebrated a crucial win.
Last weekend, Aubameyang left Wembley dejected after his last-minute penalty was saved by Spurs keeper Hugo Lloris to deny Arsenal victory in the North London derby.
Against United, he stepped forward and beat De Gea from the spot to seal a first victory over United in six league and cup meetings.
It was awarded after Fred’s forearm nudged into Lacazette, sending the French forward tumbling inside the box.
Lacazette inspired one of Arsenal’s finest days under Unai Emery’s command.
The Gunners were sharp, lively and industrious as they made amends after United eliminated them from the FA Cup six weeks ago.
Emery named six players who started Thursday’s Europa League defeat by Rennes in his starting line-up, but there was little sign of fatigue as the hosts came flying out of traps.
They opened the scoring with their only shot on target in the first half, Xhaka deceiving De Gea with a shot that left the United keeper rooted to his line.
