On a frustrating night in Tallinn, the visiting captain endured some moments to forget in front of goal aside from the 73rd minute, when his set-piece bagged Roy Hodgson’s side the points and maintained the perfect start to the campaign.
Slovenia’s 2-0 victory in Lithuania later in the evening resulted in a three-point cushion for England at the top of Group E.
It was Estonia who crafted the game’s first opening – Sergey Zenyov finding himself in a worrying amount of space in the very first minute before dragging wastefully into the side-netting from 12 yards.
England gradually asserted themselves in possession and Rooney passed up two opportunities in the space of two minutes – first volleying over from a sweetly-lofted Jack Wilshere pass and then failing to connect with an inviting Leighton Baines delivery when well placed.
Zenyov was the victim of an ugly follow-through by Cahill in the 18th minute but England were soon back in possession and creating chances – Fabian Delph lashing over from the edge of the area and Danny Welbeck’s cross-shot forcing Sergey Pareiko to tip the ball agonisingly out of Adam Lallana’s reach.
Rooney headed a Delph cross wide of the mark before the break but the visitors were handed fresh impetus after it when home captain Ragnar Klavan, booked for a crude barge on Welbeck in the first period, hauled down Delph in full flight and was duly dismissed for a second yellow card.
England failed to seize the initiative as Estonia withdrew further into their own half and defended their goal manfully – prompting Hodgson to throw on Alex Oxlade-Chamberlain and Raheem Sterling either side of the hour-mark.
It was the former who should have opened the scoring in the 69th minute when he rose all alone six yards out to meet a pacy cross from Calum Chambers, mis-timing his jump and seeing the ball spin off his back to safety.
Relief arrived in the 73th minute when Sterling was fouled right on the edge of the home box and Rooney, who had launched an earlier set-piece horribly high and wide, whipped the ball home at the near post via the bundling dive of Pareiko.
England showed little inclination to commit men forward in search of a second – instead opting to keep possession, although Rooney should have done better than fire a masterful injury-time pass from Wilshere straight at Pareiko when clean through.