Cole's goal was more than England deserved and did not fool part of a home crowd who booed off England and had earlier given Frank Lampard the same treatment when he was substituted.
England's performance will also have given boss Fabio Capello plenty to think about before the qualifying campaign for the next World Cup starts against Andorra on 6 September and against Croatia four days later.
The Italian has made it clear he wants his side playing as a unit and the players mirroring their club form for their country.
There was scant sign of those qualities during the game and, although Capello is aware of the problem, he has yet to find a way of solving it.
England had shown some brief promise at the start but it proved a false dawn as the visitors had the best of the early chances.
Some quick, intricate passing exposed England right-back Brown and Radek Sirl's cross was deflected before Stanislav Vlcek mistimed a shot just wide at the far post.
Steven Gerrard delivered an immediate riposte for England when he cut in from his role on the left of midfield and drove a shot which keeper Petr Cech scrambled wide.
But the Czechs were the more assured and imaginative as they got into their stride and a snapshot from Baros on the half-volley after a ball over the top brought a smart save from David James.
The warning signs from the Czechs were clear and they took the lead when they again worked Sirl into space down the right of England's defence.
Sirl crossed low for Baros and, with his back to goal, he turned marker Terry and saw his goalbound shot go in off Ashley Cole.
Baros put Czech Rep ahead against an England side who struggled at Wembley
Defoe had a shot saved, while Gerrard and Rooney each tried their luck from long range without success as England lacked the incisive edge of their opponents.
Capello was probably preparing some strong words for his players at half-time but his mood will have been calmed by Brown's equaliser.
The defender made amends for his role in the Czech goal by beating Tomas Ujfalusi to David Beckham's cross and powering in a header just before the interval.
Defoe paid the price for England's lack of attacking threat at the break when he was hauled off for the more physical Emile Heskey.
But England did not look secure defensively and fell behind again when Jankulovski curled in an immaculate free-kick on 48 minutes.
Keeper James gave an even shakier look to England's defence when he ran out of his goal and was beaten to the ball by Vaclav Sverkos.
Sverkos could have left James red-faced but put his effort wide for a Czech side who had little trouble keeping an unbalanced England at arm's length.
That was until they failed to clear a corner and Joe Cole squeezed a shot home among a melee of players.
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