Selby had won PTC event 4 and the Shanghai Masters in recent weeks to move up to top spot in the world rankings but found it hard to find any rhythm against the workmanlike Ebdon.
Ebdon took control early after winning three of the first four frames but Selby hit back to level and a break of 63 in the sixth frame saw him bring it to 3-3.
However, Ebdon then produced a break of 70 in the final frame to seal to win and seal his place in the last four.
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In the semis he will face Scotland's Graeme Dott in what will be a repeat of the 2006 World Championship final.
Dott sealed his spot in the final by ending the hopes of home favourite Igor Figueiredo with a 4-2 victory.
The other semi-final will see another two former world champions square off with Stephen Hendry taking on Shaun Murphy.
Henry rolled back the years in impressive fashion to white wash Ali Carter 4-0, while Murphy was too good for Ricky Walden as he enjoyed a 4-1 victory.
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