Walcott has been in top form for Arsenal, scoring four goals since being moved up front for the Gunners.
The 26-year-old had to settle for a role out wide on Friday but he still proved deadly, turning home a great pass from Ross Barkley to score the first goal.
Raheem Sterling then scored his second England goal to round off the victory, which came in front of an impressive crowd of 75,427 at Wembley.
The manner of England's first-half play was not so impressive.
For the most part, they could not puncture an organised and hard-working Estonian team, who stand 87th in the FIFA rankings.
However, there were flashes of brilliance, mainly from the electric feet of Barkley.
The Everton midfielder was frustrating to watch at times. Roy Hodgson complained he gave the ball away too much for the national side last year and he did so on a few occasions on Friday.
But when he charged at the Estonian defence, he looked like a young Wayne Rooney did in his pomp and he deservedly won the man of the match award.
England will come up against tougher opposition than this - and the Lithuanian side they will play in their final Euro 2016 qualifier on Monday - but they now have nine wins from nine matches and no one can complain about that.
If they beat Lithuania in Vilnius, they will become the sixth side in history to qualify for the European Championship with a pristine qualifying record.
Rooney, out with an ankle injury, received a huge round of applause when he collected a golden boot from Sir Bobby Charlton before kick-off for breaking his scoring record.
After the pair retreated to the stands, the cheers gave way to silence as a dull opening half ensued.
Walcott volleyed at Mihkel Aksalu and Barkley fluffed two chances to beat the Estonia goalkeeper.
A brief moment of alarm was caused in the home defence when Taijo Teniste gained space in the box, but Chris Smalling blocked his shot.
England are 11/1 fifth favourites to win Euro 2016 with Sky Bet after making it nine wins out of nine in their qualifying group.
Meanwhile, man of the match against Estonia, Ross Barkley is 1/3 to make Roy Hodgson's final 23-man squad for the trip to France.
Dele Alli is 5/2 to be named in that squad after making his debut as a second-half substitute in the 2-0 Wembley win.
England were dominating possession but there was little excitement. Those who popped off early for their half-time pie missed the breakthrough, however.
Just when it looked like the Estonians had managed to hold out for the first half, Barkley sliced open the visitors' defence to find Walcott, who took one touch before rolling the ball past Aksalu.
Barkley brought the home fans to the edge of their seats with a 40-yard sprint but he was dispossessed when he had options at either side of him.
The midfielder redeemed himself somewhat moments later when he drifted in from the right flank past two Estonians and unleashed a powerful left-foot drive that whistled by Aksalu's far post.
Barkley landed his next shot - another high drive - on goal but the Estonian stopper scrambled to his right and tipped it over the bar.
Hodgson brought Alex Oxlade-Chamberlain and Jamie Vardy on to inject some life into the game and it was the Leicester forward who helped put the win beyond doubt five minutes from time.
Vardy latched on to Kane's flick-on from a long punt up field from Joe Hart and he squared for Sterling, who had the simplest of finishes.