Luka Milivojevic put the hosts ahead from the penalty spot in first-half stoppage time at Selhurst Park but Xhaka levelled with a venomous free-kick and Pierre-Emerick Aubameyang gave Arsenal the lead amid strong handball claims against Alexandre Lacazette.
But there was a sting in the tail as Xhaka – playing in the unfamiliar position of left-back – brought down Wilfried Zaha and gave Milivojevic the chance to make it two out of two from 12 yards.
The Switzerland international initially protested to referee Martin Atkinson but accepted he was in the wrong afterwards.
"It's difficult. I think it's a clear penalty," Xhaka told Sky Sports. "I touched him in the knee.
"The referee gave a penalty. That's football."
After his goal, Xhaka ran off to celebrate with Unai Emery – his head coach having enquired why he was not on dead-ball duties during the first half.
"I heard something from the coach in the first half. He asked me why I wasn't taking the corners and the free-kicks," said Xhaka.
"It was the first free-kick of the second half, I took it and I scored.
"I wanted to say thank you. I heard [Emery] enough in the first half. He told me I must take the free-kicks and the corners."
The result meant Arsenal's winning streak in all competitions was halted at 11 but, on balance, Xhaka was happy to accept the point.
"We know we can't win all the games. We try," he added.
"It was not our best performance but one point here… alright. We take the positive things from this game and move forward."