England 1 ............ Ecuador 0
Beckham crashed his shot home from 35 metres on the hour mark of what had been a moribund second round game played in sticky conditions at the Gottlieb-Daimler-Stadion.
Victory means Sven-Goran Eriksson's men now play either the Netherlands or Portugal, who were meeting later on Sunday, in a quarter-final on Saturday in Gelsenkirchen.
Beckham became England's first player to score in three World Cups. He was sick on the pitch during the second half and said he had not being feeling well before the game.
Ecuador coach Luis Fernando Suarez was gracious in defeat.
“In football sometimes you lose not because if mistakes you made a mistake but from a great free kick which was the case today,” he told reporters.
“I think we played very well in this World Cup. Our objective was to make the second round and we did that. We're satisfied but we always thought we could achieve something more”
England were playing in a 4-5-1 formation with Wayne Rooney as a lone striker and Michael Carrick making his competitive England debut as a holding midfielder.
With Michael Owen out of the finals with a knee injury, the theory was to allow Steven Gerrard and Frank Lampard to get forward in support of Rooney.
The practice was that England failed to create a single goalscoring opportunity in a scrappy first half and were lucky not to go in at the break a goal down.
John Terry's poor headed interception after 11 minutes fell to Carlos Tenorio and the Ecuador striker had only keeper Paul Robinson to beat.
But Tenorio took a second too long and his deflected shot, under a challenge by Ashley Cole, hit the bar and flew over.
Ecuador, who reverted to the side which beat Costa Rica 3-0 to reach the last 16, looked sharper with strike pair Agustin Delgado and Tenorio back in the side.
England's passing, which was often poor before the break, failed to improve afterwards.
Sven-Goran Eriksson's men, who seemed intent on boring the South Americans into submission, finally got the breakthrough when Beckham's free kick flashed past keeper Cristian Mora, grazing the inside of the post.
It brought the game to life and England were only let down by the final pass in their attempts to add a second on the break in the closing stages as Ecuador pushed forward.
Scorer: England – David Beckham 60.
Halftime: 0-0, Attendance: 52,000.
Teams:
ENGLAND (4-5-1): 1-Paul Robinson; 16-Owen Hargreaves, 5-Rio Ferdinand, 6-John Terry, 3-Ashley Cole; 7-David Beckham (19-Aaron Lennon 87), 8-Frank Lampard, 18-Michael Carrick, 4-Steven Gerrard (20-Stewart Downing 90+2), 11-Joe Cole (15-Jamie Carragher 77); 9-Wayne Rooney.
ECUADOR (4-4-2): 12-Cristian Mora; 4-Ulises de la Cruz, 3-Ivan Hurtado, 17-Giovanny Espinoza, 18-Neicer Reasco; 8-Edison Mendez, 20-Edwin Tenorio (7-Cristian Lara 69), 14-Segundo Castillo, 16-Luis Antonio Valencia; 11-Agustin Delgado, 21-Carlos Tenorio (10-Ivan Kaviedes 71).
Referee: Frank De Bleeckere (Belgium).
Linesmen: Peter Hermans and Walter Vromans (both Belgium).—Reuters