Logan beat Jefferson in the finals the past two seasons.
With one out in the fifth and the score tied at 1-1, Wooten hit a line drive to the left field gap. Jefferson center fielder Brian Peterson dove and missed the ball, which scooted to the wall.
Both Gertz and Jefferson coach John Lowery said Peterson might have kept Wooten from scoring if the center fielder didn't leave his feet.
"I thought I was going to get to it," said Peterson, a junior. "I was kind of upset, but I'm looking forward to being out here next year."
Logan starter John Ryan Steele held third-ranked Jefferson (32-9) to six hits.
In the earlier game, Brandon Halstead pitched a five hitter, striking out nine and walking none. He also scored both of Hurricane's runs in the first and sixth innings. Daniel Carte got two of the Redskins' four hits.
John Marshall coach Bob Montgomery missed the tournament due to a death in the family. Assistant coach John Rush led the team in the interim.
"I said all year if we can make two or less errors and walk four or less batters, as long as they're not all in the same inning, we'd win," Rush said. "Today, the errors, they got us."
Unranked John Marshall (20-12) committed four errors and didn't get a runner past second base.
The loss spoiled a three-hitter by John Marshall left-hander Henry Morgan.
On Friday, Hurricane's Travis McGrath (8-0) will pitch against Logan's Derrick Lambert (7-2).
Hurricane lost two of its three meetings with Logan during the regular season. Hurricane was shut out in one of those losses and was held to one run in the other.
Hurricane hasn't been to the championship game since 1999, when it lost to Jefferson. But coach Billy Joe Hicks, who will coach his final game on Friday, doesn't believe his players' lack of championship experience is a disadvantage.
"Our leaders are Halstead and Carte. They've been in big situations in big games. They'll still come through for us. That's how much I believe in those two kids," Hicks said.
While Hurricane has been ranked No. 1 in The Associated Press state baseball poll for most of the season, Logan and Jefferson have won the last four Class AAA titles. So most of the statewide attention in this tournament has been off Hurricane.
"I think we kind of have been overlooked," Halstead said. "Logan and Jefferson, they're always going to be here."