Youzhny needed 2 hours, 42 minutes to stave off eighth-seeded massive-serving Croat Ivo Karlovic, 7-6 (12-10), 3-6, 7-6 (8-6). The 6-foot-10 Karlovic swatted 22 aces in a losing effort.
Up next for Youzhny will be last year's Zagreb runner-up Michael Berrer, who moved within one victory of his second straight trip to the final here with a 5-7, 6-4, 6-4 come-from-behind win over Austrian qualifier and fellow left- hander Jurgen Melzer.
Berrer lost to Croatia's Ivan Dodig in last year's finale.
Dodig will not be a repeat champion this year, as the fourth seed was knocked out by a sixth-seeded Baghdatis, 6-4, 7-5. The former Australian Open runner- up Baghdatis titled here back in 2007.
Baghdatis will appear in his second semifinal in four events so far this season.
The 2012 Zagreb champion will collect $90,000.