Published: 2020-02-24 01:10:15 BdST
The win moves Mikel Arteta's Arsenal side up to ninth place in the league and back in the battle for European places, while Everton remain without a win at the Gunners in 24 years.
As well as the goals of the prolific Aubameyang, who is now joint top scorer in the league on 17 goals with Jamie Vardy, Arsenal had keeper Bernd Leno to thank for some late saves which preserved the lead.
Dominic Calvert-Lewin put Carlo Ancelotti's team ahead in the first minute with a superb, acrobatic volley after David Luiz had failed to deal with a Gylfi Sigurdsson free kick.
But Arsenal reacted well, with young forward Eddie Nketiah, who started ahead of Alexandre Lacazette, levelling in the 27th minute, his first goal at the Emirates coming from a fine cross from the left from substitute Bukayo Saka.
Six minutes later and Arsenal were ahead -- Luiz making amends for his earlier mistake with a lovely, defence-splitting pass to Aubameyang who calmly slotted past Jordan Pickford.
Brazilian Richarlison brought Everton back on level terms though just before the interval, poking home from close range.
But Arsenal struck straight after the break with Aubameyang heading in a Nicolas Pepe cross, 23 seconds after the restart.
Leno then produced a brilliant point-blank reflex save from Calvert-Lewin and did well to keep out a Richarlison effort as Everton pushed for an equaliser.
Arsenal went close to a fourth goal when Nketiah, who spent the first half of the season on loan at Championship (second-tier) Leeds United, struck the bar with a curling shot.
Everton almost grabbed a point at the end but Calvert-Lewin's header from a Bernard cross was just wide of the post.