Aston Villa looked to have taken an early lead in the opening minutes through a smashing shot from John McGinn, but the goal was chalked off after the referee consulted VAR and determined that Ross Barkley was offside and had obstructed Arsenal keeper Bernd Leno's view.
The visitors did take the lead later in the first half when Bukayo Saka inadvertently redirected the ball into his own net from a cross after a nice bit of build-up play from Villa.
Villa continued to look like the better side as the second half started and were eventually awarded for their dominance with a pair of goals from Ollie Watkins to extend their lead to three and put the match away.
Two consecutive defeats had halted Villa's early-season charge, but they moved back up to sixth with 15 points from seven games. Inconsistent Arsenal are down in 11th with 12 points after four wins and four defeats so far.
The win marks Villa's best start to any season in 22 years.
"We've conceded a few goals the last couple of games and it's how you bounce back and we've done that tonight," Watkins, who signed from Brentford in the transfer window, said.
"You've seen tonight and against Liverpool, we're a great side and we can beat anyone."
After the match, Arsenal boss Mikel Arteta said: "The way we lost today really hurts."