The England captain curled home a free-kick 17 minutes from time on his 99th international appearance at the A Le Coq Arena in Tallinn on Sunday to ensure Roy Hodgson's side maintained their 100 per cent record in Group E.
Rooney's 43rd international goal extended England's perfect start after they had endured a frustrating second half following Estonia captain Ragnar Klavan's red card three minutes into the second half.
England were dominant in the first half, but failed to make it count and, although they were not at their best after the break, Rooney's strike was enough to secure another three points and they are yet to concede a goal in qualification.
For Estonia, it was a second successive defeat, while group leaders England will be looking to make it four wins out of four against Slovenia at Wembley next month.
Adam Lallana, Leighton Baines and Fabian Delph came into the England side as Raheem Sterling was rested, while Kieran Gibbs and James Milner also dropped to the bench.
Artur Pikk made his first senior competitive start for Estonia as one of three changes to the side that was beaten 1-0 by Lithuania on Thursday, with Ken Kallaste suspended following his sending off.
Hodgson said ahead of the game that Estonia might surprise a few people and they almost gave the England boss a nasty shock when they went close in the first minute.
Delph appeared to be fouled in the Estonia half, but referee Marijo Strahonja waved play on and Sergei Zenjov's shot was deflected just wide off Gary Cahill at the near post after a swift break.
Henri Anier volleyed over from the resulting corner, but England soon stamped their authority on the game and Rooney fired just over the crossbar after Jack Wilshere picked him out with a clever ball over the top of the Estonia defence.
An unmarked Rooney then failed to make any contact with an inviting Baines cross 17 minutes in when he really ought to have scored as England knocked the ball around with confidence.
The impressive Wilshere burst forward from midfield and surged into the penalty area before firing a right-footed strike narrowly wide of the near post nine minutes before the break.
Estonia had been up against it in the first half and their chances of getting anything out of the game suffered a major blow three minutes into the second period, when defender Klavan was shown a second yellow card for obstructing the onrushing Delph as the midfielder broke forward at pace.
Hodgson replaced Delph with Alex Oxlade-Chamberlain on the hour mark and Sterling came on for Liverpool team-mate Jordan Henderson soon after as England strived to make a breakthrough.
Cahill headed a corner over the crossbar and Oxlade-Chamberlain then should have done better when Calum Chambers' cross from the right picked him out, but he failed to make a proper contact with an attempted header.
England were unable to pose the same attacking threat that they showed against 11 men in the first half, but they were finally in front when Rooney curled a free-kick just inside the near post that goalkeeper Sergei Pareiko failed to keep out after Sterling had been upended just outside the penalty area.
Rooney missed out on the chance to add a second in stoppage time when he failed to beat Pareiko after Wilshere had picked him out with a lovely pass, but his free-kick was enough to secure the victory and edge him a step closer to Bobby Charlton's England goal record of 49.
