Reigning champion Murphy hit by the Crucible curse.
Ebdon raced into a 7-1 lead in session one and though Murphy improved in the second to be only 10-6 down, there was to be no comeback.
He won only one frame in the evening session to bow out 13-7 as the Crucible curse of first-time champions defending the title struck again.
But in a repeat of what had happened on Tuesday, Ebdon again missed a fine chance of a maximum 147 break - and this time got even closer.
In frame seven the 2002 champion had potted 12 reds and blacks but missed the next pot to a middle pocket when bridging over a ball.
He got to the final red in frame 11 with the ball just above the brown spot, but rattled it in the jaws of the green pocket.
Despite squandering the chance of the pounds 147,000 prize for the maximum, Ebdon was not distracted and completed a comfortable success before applauding Murphy out of the arena.
'I did that because I really appreciate everything Shaun has done for snooker as world champion over the last 12 months,' said Ebdon, who now lives in Dubai.
'He has put himself out for the game and done an outstanding job, and I wanted to say thank you for that.'
As for tonight's 147 attempt, he added: 'What a nightmare! I put a touch of left-hand side on the shot and just caught it too thick.'
On the ovation he received from his local crowd and from his opponent after his defeat, Murphy said: 'It was really nice to have that and to be cheered out. It's been quite an emotional day but not all in a bad way.
'The first session will haunt me for a few weeks and I've no idea why I played so badly in it. But Peter is on top of his game and is my tip to win the title now.'
Earlier, Marco Fu became only the second Asian player to reach the semi-finals of the 888.com World Championship by recording a shock 13-10 victory over Ken Doherty.
The Hong Kong player emulated James Wattana as he maintained his status for being the tournament's surprise package, and now only Peter Ebdon or Shaun Murphy stands between him and the final.
Doherty, so impressive against Matthew Stevens in the second round, was hot favourite to win the match and at 8-6 up looked set fair to go on and complete a resounding win.
But Fu, a 125-1 outsider at the start of the tournament, has been producing some composed break-building in Sheffield and when he made a 110 to level it at 8-8 it was clear he would not lie down.
Today's play was largely tactical and two consecutive frames, which took the score to 10-10, lasted a total of an hour and three quarters.
After the interval, however, the 28-year-old qualifier took his chances when among the balls and contributions of 60 twice and 75 secured his progress.
'The frame I won to make it 10-10 was massive because Ken had come from three snookers down to steal the previous one,' said the world number 24.
'The interval then came at the right time for me. I went to the dressing room, composed myself and came out really strongly. I had been prepared for it to go to the wire.
"I've never thought about winning the tournament. I came here with only one goal - to enjoy myself because I haven't been doing that. I've been struggling in tournaments.
"But working with my coach Terry Griffiths has brought a lot of improvement and the hard work is really paying off."
Doherty admitted he had missed out on a golden opportunity to repeat his 1997 World Championship triumph.
"I blew it," said the Irishman. "I can't grumble because I had my chances.
"I'm very disappointed to have played the way I did after my performance against Matthew Stevens. I lost a lot of silly frames early in the match and sometimes they come back to haunt you. But I have to take my hat off to Marco. He played well tactically and made some good breaks. If he keeps doing that he can beat anyone."
Earlier, Graeme Dott thwarted a magnificent fightback from Australia's Neil Robertson to reach the semi-finals for the second time in three years.
The Scot let slip leads of 10-5 and 12-8 as Robertson forced a deciding frame before going through 13-12 to book a clash with Ronnie O'Sullivan, his conqueror in the 2004 final, who beat Mark Williams 13-11.