The tie, which is a repeat of the 2009 Challenge Cup final won by the Wolves, will be played at the Halliwell Jones Stadium on Thursday.
The announcement, which was made by Warrington chairman Stephen Broomhead at a press conference broadcast live by Sky Sports News from the Halliwell Jones Stadium, means Wigan will meet Leeds in the second semi-final at the DW Stadium on Friday.
Although Huddersfield finished top of the table - for the first time for 81 years - it was no surprise that they were chosen by the Wolves, who have already beaten them three times this year.
In addition to completing a league double, Warrington hammered the Giants 44-24 in the Challenge Cup quarter-finals in July.
“After very careful consideration, we have decided to play Huddersfield Giants,” said Broomhead.
“The decison was made that we would choose the winners of the Huddersfield-Hull game.”
Leeds will go to the DW Stadium with confidence, having won 20-6 there in the final match of the regular season earlier this month.
Warrington coach Tony Smith, who has consistently stated his opposition to the concept, was once more absent from the proceedings, with the Wolves represented instead by his assistant Willie Poching and captain Adrian Morley.
Broomhead said the decision was made by the Warrington board and supported by the coaching staff.
Huddersfield coach Paul Anderson, who was critical of the three-day wait to discover his side’s semi-final opponents, said: “We’ve got a challenge now.
“Warrington obviously feel they can beat us so we’ve got to knuckle down and prepare for Thursday.”
The Wigan-Leeds tie is a repeat of the inaugural Grand Final in 1998, which was won by the Warriors.
Leeds coach Brian McDermott said: “We’re really excited to be in this position. We went to the DW Stadium a couple of weeks ago and it was a cracking game which took a few lumps out of us. It’s going to be a big ask for us.”
The Rhinos have major doubts over forwards Jamie Jones-Buchanan and Brett Delaney after they picked up knee and groin injuries respectively in Friday’s 11-10 win over St Helens.
“They’re not good, either of them,” McDermott said. “But I don’t want to write them off just yet and we will give them until the 11th hour.”