Beckham stepped up to deliver an unstoppable shot on the hour mark as England saw off their opponents despite a shaky performance.
England will take on the winners from Holland and Portugal who will play later on the same day.
Underdogs Ecuador were better in the first period and missed two rare opportunities to stun Sven-Goran Eriksson's side who failed to find their flow with a 4-5-1 formation.
Carlos Tenorio almost put Ecuador ahead in the 11th minute when he scuffed a loose ball after a poor clearance by John Terry but his shot hit the woodwork thanks to a last-second challenge from Ashley Cole.
England were lucky not to concede minutes after when Edison Mendez's free-kick deflected off Agustin Delgado and went just wide.
In the 60th minute, the Real Madrid midfielder curled a 35-meter ball over the wall and despite a full stretch from goalkeeper Cristian Mora the ball squeezed into the narrow angle for England's winner.
Luis Antonio Valencia answered quickly but his long-range bullet was blocked by goalkeeper Paul Robinson.