The Frenchman started with captain Laurent Koscielny, Rob Holding and Gabriel Paulista at the base of his defensive set-up at the Riverside Stadium.
The tactical move seemed to pay off, as the Gunners ended their misery on the road in the Premier League.
Alexis Sanchez and Mesut Ozil scored either side of an Alvaro Negredo finish, to move Arsenal into sixth place on the table.
When asked after the game about his new system, Wenger replied: “It added more stability on the long balls. Recently we’ve been punished on that. [Is it permanent?] No.”
It remains to be seen if Arsenal will use the 3-4-3 when they take on Manchester City in the FA Cup semi-final this Sunday.