Brighton came from a goal down to topple the Gunners who went ahead through Nicolas Pepe in the 68th minute, before goals from Lewis Dunk and Maupay turned the game.
Maupay scored deep into second-half stoppage time to clinch the win, which leaves Arsenal in 10th spot and with back-to-back defeats after their midweek loss to Manchester City.
However, Maupay tangled with several Arsenal players after the full-time whistle, led by Matteo Guendouzi, after falling easily as Brighton tried to milk the clock in the dying stages.
Maupay had also earlier been involved in an aerial challenge with Gunners keeper Bernd Leno, which forced the German to be stretchered off with a suspected knee injury.
Brighton’s match-winner controversially said Arsenal “got what they deserved” and “need to learn humility” after the late winner, as emotions boiled over.
Arteta responded: “He can say whatever he wants, I know my players and one aspect that they don’t miss for sure is humility.”
The Spaniard added that Arsenal had no one to blame but themselves for the defeat.
“We gave the first goal away and we lost a few important duels afterwards, so I think its all our fault,” Arteta said.
Arteta also provided an update on Leno, who was carried off and replaced in the 40th minute with Damian Martinez, and refusing to blame Maupay.
“I believe that no player has the intention to hurt anybody and I believe in this case its exactly the same, it was unfortunate,” Arteta said.
“Bernd’s injury doesn’t look good and we will have to assess him probably tomorrow, but it can happen on a football pitch. It’s a knee injury, I think he had a hyperextension of the knee and we have to assess the damage.”
Leno pointed at Maupay as he was being stretchered off, suggesting he was squarely laying the blame on him for his unfortunate landing, but the Belgian offered his sincere best wishes post-game.
“Until the keeper gets the ball you never know what could happen,” he told BT Sport.
“I just went to get the ball really. I think it was shoulder against shoulder and when he landed he twists his knee, you know its football, there’s contact.
“I never meant to injure him so I’m really sorry. I apologise again and wish him a speedy recovery.”
Elsewhere, third-placed Leicester City and Watford both scored late in a 1-1 draw, while Bournemouth’s relegation fears worsened with a 2-0 loss at home to Crystal Palace.
West Ham United also missed an opportunity to ease their relegation concerns with a 2-0 home defeat to Wolverhampton.