Jermain Defoe put Spurs in control and they should have added more before City substitute Valeri Bojinov claimed his first goal of the season. But Keane ended City's Europa League aspirations when he beat fellow Irishman Shay Given from the spot.
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Afterwards Mark Hughes, who criticised the decision to award the penalty, also tried to put an end to speculation over his future when he said: 'I have been totally frustrated and bemused from day one. It's got to the stage where everyone has to understand Mark Hughes will be the manager of Manchester City next year. The speculation over my future has made my job harder than it already is.'
Spurs dominated the first half with only Given standing between them and an embarrassing half time score. He denied Defoe, Roman Pavlyuchenko and Ledley King before Defoe broke the deadlock. Tom Huddlestone delivered the crucial ball and Defoe, with his back to goal, back-healed beyond Given.
And soon afterwards Defoe was involved in a strange incident. Challenging Nedum Onuoha, he slipped then appeared to kick assistant referee Trevor Massey, who fell dramatically, holding his ankle in agony.
Defoe was lucky not to be punished by referee Mark Halsey, who saw the funny side, as did Robbie Keane, who comically accused the linesman of diving, while the fans sang 'Are you Drogba in disguise.' Massey stayed on until the interval before being replaced by fourth official Stuart Attwell.
Hughes brought on strikers Valeri Bojinov and Benjani, and the changes made an instant impact. In the 65th minute the ball came off Benjani's head and fell to Bojinov who responded with a left-foot volley into the top left hand corner.
It was the first goal conceded by Spurs at White Hart Lane in seven games, and 10 hours and 38 minutes, and Oasis star Liam Gallagher could not contain his delight, responding with a gesture suggesting the outcome would be 2-1.
But Gallagher's prediction came back to haunt him near the end when substitute Fraizer Campbell – on loan from Manchester United – was fouled by Micah Richards and Keane converted.