Mertesacker was one of four players who suffered a sudden bout of flu ahead of top-of-the-league Arsenal's visit to the reigning champions after falling ill the night before the match at Old Trafford.
The towering centre-back's place in the starting line-up was taken by Belgium international Thomas Vermaelen as Arsenal slipped to a 1-0 defeat allowing United to move to within five points of the North London side.
At this stage Mertesacker has not been ruled out for the Germany's friendly against Italy in Milan this coming Friday nor their visit to Wembley to take on England four days later.
It appears increasingly unlikely the German will link up straightaway with his national side who are gathering in Munich.
The German football federation says it remains open whether the Arsenal defender will join the team at a later date.
Thomas Rosicky also missed the Manchester United game with his place in the starting line-up taken by Mathieu Flamini.
Mikel Arteta and Serge Gnabry were the two other players who fell ill. Arteta was fit enough to start the game although he was replaced by Gnabry in the 82nd minute of the final Premier League game before the international break.