Rumours grew that the German World Cup winner had had a disagreement with Emery after he learnt he was to be left out of the starting line-up at the Emirates, but Emery said he still had a good relationship with the 29-year-old, who he said had withdrawn because of illness.
"No problem with the player. It isn't true, that information," Emery told reporters. "I don't know who started it but if you ask me, the doctor, or the club, he was sick.
"He left training because he was going home. He was sick. Today he was here. I said come if you feel better and he felt better. Before the match he was with the team and with me. Ask the doctor. He can explain better."
After back-to-back losses against Manchester City and Chelsea, Arsenal were in desperate need of a positive response.
The Gunners, however, went 1-0 down to Marko Arnautovic's effort from outside the box before a Nacho Monreal strike, Issa Diop's own goal and Danny Welbeck's late effort sealed a 3-1 victory.
Emery said afterwards that his side were still in the midst of a transition period following the departure of long-term boss Arsene Wenger, but would be buoyed by the first victory of his reign.
"We need to improve in this transition to get the balance, to get more control with the ball," Emery told the BBC.
"West Ham are a good team. It was a difficult match. For that we are happy but there are things to improve. But also, the win gives the confidence for the players. The three points were very important. It was very important for our supporters."
While many Arsenal fans will have been breathing a sigh of relief after their indifferent start to the season, bottom-of-the table West Ham and boss Manuel Pellegrini are still searching for their first points.
"I am very happy in the way we played, we played well with good pace and movement, so I am sure soon it will come," he told the BBC.
"We improved on what we did in our two first games. We need to add points, but we are going to continue searching."
(Reporting by Tom Hayward,; Editing by Neville Dalton)
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