Xhaka, who Emery has confirmed as club captain, was strongly criticised on social media following United's opening goal at Old Trafford, where Arsenal held the Red Devils to a 1-1 draw.
The Switzerland midfielder appeared to duck out of the way of Scott McTominay's rasping 20-yard drive, although some replays indicated the ball took a small deflection to divert it away from his head.
Arsenal head coach Emery, though, gave Xhaka his full backing after Pierre-Emerick Aubameyang's seventh Premier League goal of the season earned the Gunners a point.
"He worked with a big commitment," Emery told a news conference after Arsenal moved back into the table's top four.
"He ran back, maybe the first run back in this action. I didn't see that action [the apparent duck].
"I watched when he was running back and really he did perfect with that run."
With Alexandre Lacazette again ruled out by injury, teenager Bukayo Saka took his chance to shine by setting up Aubameyang for an that was equaliser initially disallowed for offside, then given by VAR.
"He is working and improving, being mature and playing matches," Emery, who left Mesut Ozil out of his squad, said of the 18-year-old.
"With his work it's natural. He's improving, he’s helping us now as an important player.
"We are going to go with him with calm and patience but also if he deserves to take minutes to have that confidence to help us, it's fantastic for us."
Arsenal came from behind for the second Premier League game in a row after a 3-2 home defeat of Aston Villa last time out and Emery hailed his team's fitness levels.
"Football is changing. Physically it's very important. Every team physically is very strong," Emery added.
"You need to play with quality, you need to play with quality of course and be able to use the space on the pitch for 90 minutes.
"Every player in each team is very, very fit. We both have very quality players. We need to improve our mental work, tactically to achieve the best performance."