The Ghana midfielder was making his return from a thigh injury which had kept him out since November 5.
But Partey lasted only until half-time before being substituted.
"I applaud their first goal, it is world class, but the second goal we are a man down, we leave a massive gap and they take advantage," Arteta told the BBC.
"He [Thomas Partey] has to stay on the pitch. It looks like the same injury he has already had, he will have an MRI."