Liverpool duo Joe Cole and Glen Johnson were overlooked, although the latter had only recently recovered from a groin injury.
Rooney made a goal for Joe Cole and scored himself late on after Jermain Defoe had given Fabio Capello's side an early lead against the local side.
The travelling England fans showed their discontent as the players came off at the interval and, unsurprisingly, Capello made changes - replacing the Downing with Joe Cole and sending Emile Heskey on in place of Defoe.
He may have left established players such as Joe Cole and David Beckham on the bench here with Wednesday's game in Croatia match in mind but it will worry him that their replacements struggled against such unheralded opposition.
Just 34 minutes were on the clock when Chelsea racked up their fourth - Lampard stretching to volley home Ashley Cole's cross - and Ballack, Joe Cole and Anelka again all failed to finish off flowing moves as Chelsea moved the ball about at will.
Chelsea boss Mourinho immediately sent on Geremi for Joe Cole, and also replaced the injured Hernan Crespo with Didier Drogba at the start of the second half.
He has lured Joe Cole to Anfield and persuaded key duo Steven Gerrard and Fernando Torres to stay with the club.
They suited 4-3-3 and they had their best seasons when they had Joe Cole on the right and Arjen Robben on the left.
BBC: SPORT | Football | Premier League | Alan Hansen's column
Even so, Kalou, Jon Obi Mikel, Joe Cole, Ballack and Zhirkov all either forced regulation saves from Robinson or missed the target before the break.
Even with Gerrard, Torres and Joe Cole in the starting line-up, Liverpool attacks were in short supply and Rovers took a deserved lead on the half-hour mark.
And with Tottenham's Aaron Lennon still suffering from a groin problem, Capello may now turn to both Theo Walcott and Shaun Wright-Phillips to cover the right side of midfield, with James Milner, Joe Cole, Stewart Downing and Adam Johnson also in the reckoning.
By contrast, Estonia's defence looked extremely vulnerable, with Rooney and Joe Cole particularly dangerous.
Also included by Capello are John Terry, Rio Ferdinand, Joe Cole, Aaron Lennon and goalkeeper Rob Green.
Goals from Joe Cole, Peter Crouch and Michael Owen earned a vital victory against a determined Estonia side.
Only Joe Cole, Salomon Kalou and Jon Obi Mikel remained from the team that defeated Arsenal on Sunday.
BBC: Chelsea boss Carlo Ancelotti defends cup team selection
Gerrard was replaced by Joe Cole after an hour and the Chelsea midfielder admitted he was played out of position.
Keegan admitted he had checked the likes of Frank Lampard and Joe Cole, but had decided to rely on experience.
Chelsea made a double switch with 17 minutes left, sending on Tal Ben Haim and Shaun Wright-Phillips for Ashley Cole and Joe Cole.
Kirkland saved a header from Alex, Michael Ballack drilled a free-kick over the bar and Joe Cole narrowly missed as Chelsea looked for a decisive second goal.
He came closest when he ran on to Joe Cole's dummy and produced an exquisite chip which the backtracking keeper Heurelho Gomes fantastically tipped over the bar.
Gerrard and Joe Cole wasted a golden chance to score a fourth when they found themselves two-on-one against the Estonia defence but made a complete hash of it.
BBC: SPORT | Football | Internationals | England 3-0 Estonia
While headers from Frank Lampard and Joe Cole had put Chelsea well in control in the first half, Scolari was disappointed his side did not show more discipline after the break.
Having seen what Olympiakos had to throw at them in the first period, the Blues showed greater desire to commit men forward after the break, with Ashley and Joe Cole featuring more prominently than they had earlier.
There was still 25 minutes remaining at that point, and Sunderland must have feared the worst, but Fulop denied Anelka a hat-trick from six yards out and Joe Cole hit the post with a header to give the away goal some respite.
And straight away the visitors went on the offensive, even with Didier Drogba and Deco dropped from the matchday 18, with Kalou and Ballack going close in the early exchanges and Joe Cole forcing a smart near-post save from Mildenhall after good work from Lampard.
And looking ahead to the rest of the tournament, substitute Joe Cole senses England will only get better and could even win the World Cup.
James had done his utmost to prevent the visitors extending their lead further with strong saves from shots by Lampard and substitute Joe Cole.
"There has been a constant war of minds between what Joe Cole's strengths are and what others perceived as his weaknesses, " admits the former Leeds United boss.
BBC: Can Joe Cole fulfil early promise and revive Liverpool?
The lively Salomon Kalou and excellent Joe Cole were both enjoying plenty of freedom out wide as the Blues forced five corners in the opening 15 minutes.
Joe Cole put the Reds ahead and, while Cristian Tanase equalised for Steaua, Lucas Leiva powered in a long-range strike sandwiched in between two David Ngog goals to wrap up a win for the Merseysiders.
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