Having started the season with an impressive 12-match unbeaten run at home in the Premier League, Sunderland have now lost their past two games at the Stadium of Light, failing to bounce back from their defeat to Liverpool.
Moments before Fulham's opener, Romaine Mundle was played in by Lutsharel Geertruida, but he missed the target from only a few yards out.
Nilson Angulo also had an effort touched over the bar when Sunderland were trailing 2-0.
It was a frustrating afternoon for the Black Cats, made worse by two first-half injuries.
Manager Regis le Bris lost defender Nordi Mukiele - impressive this season - and Jocelin Ta Bi, who was making his first league start for the club.
But the sight of captain Granit Xhaka returning in the second half after a four-match absence was a welcome one as Sunderland look to halt a worrying run of four losses in five league games.