We study entanglement entropy for ball-shaped regions in excited states of holographic conformal field theories. The excited states are prepared by the Euclidean path integral in the CFT with a source turned on for some double-trace operator, with a small, amplitude . On the gravity side, the double-trace operator deforms the bulk geometry as well as the entanglement structure of the state of bulk matter fields. By the quantum extremal surface formula, this leads to a deformation of the shape of the entanglement wedge, an effect which becomes manifest in the entanglement entropy at . On the CFT side, we explicitly calculate the entanglement entropy perturbatively in the source amplitude to , in terms of modular-flowed correlation functions of double-trace operators. We then evaluate these modular-flowed correlation functions using Witten diagrams. This calculation involves a Schwinger-Keldysh contour ordering prescription in the bulk, which we motivate using analytic continuation from Euclidean replica correlators. Focusing on a particular graviton-exchange diagram, we rewrite it in a form where it manifestly reproduces the canonical energy term present in the quantum Ryu-Takayanagi formula, including the shape deformation of the entanglement wedge due to backreaction and quantum effects.