Goals from Theo Walcott after 45 minutes and Raheem Sterling in the 85th gave England their ninth successive win in a qualifying campaign for the first time.
England lead Group E with 27 points from nine games, with Switzerland also qualifying after beating San Marino 7-0 to climb to 18 points. Estonia have a remote mathematical chance of finishing third after Slovenia where held 1-1 by Lithuania.
England manager Roy Hodgson told ITV: "It was as tough as we thought it would be because we have played against an organised team that are also quite intelligent in the way they play.
"We attacked a lot and saw a lot of the ball and had quite a few chances but it was a question of putting them away.
"But I think we were good value for our 2-0 win. In these type of games if you are not careful and lose your concentration you can slip up.
"People are telling me that this victory tonight will ensure we are seeded for the tournament in France and that is important too."
England were never under any threat from an Estonia side that have only scored four goals in nine matches on a generally subdued night at Wembley.
One of the high spots came before kickoff when Bobby Charlton presented fellow Manchester United great Wayne Rooney with a golden boot for breaking his 45-year-old scoring record with his 50th goal for England last month.
Rooney was out injured but England did not miss him. Ross Barkley created Walcott's opener before halftime with a superb through ball which the Arsenal man collected with a deft right foot touch before his shot gave keeper Mihkel Aksalu no chance.
Sterling doubled the lead five minutes before the end with an easy chance following a cross by substitute Jamie Vardy, who had only been on the pitch for two minutes.
(Reporting by Mike Collett; editing by Toby Davis and Ken Ferris)
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