Right fielder Trent Hanna's three-run triple that gave the Eagles a 6-5 lead in the sixth inning that they would never relinquish.
Sawyer Carroll tied the game with an RBI double in the bottom half of the inning, but Morehead scored three runs in the seventh to earn the win.
But Morehead State continued to rally, scoring three runs with two outs in the seventh to jump back on top 9-6.
The loss was just the Cats' second defeat in their last 38 regular season non-conference games, but it was a sour one.
UK committed four fielding errors that led to four unearned runs for the Eagles, who entered Wednesday's game having won just eight games all year.
"It's a tough one to lose," said redshirt freshman Keenan Wiley.
Wiley, making just the fourth start of his career, went 4-for-5 at the plate today. Though disappointed in UK's performance, Wiley said the most important thing the Cats can do is move forward and work toward getting better.
"We just have to put this behind us and learn from our mistakes," Wiley said. "We have to use what went wrong in this game and work toward getting better so we can be ready for Florida this weekend."
Things didn't appear to be all bad in the beginning.
The Cats chased Morehead starter Josh Barnes in the first inning after he just threw 31 pitches. Barnes gave up an RBI double to Mike Brown and then walked two more runs home with the bases loaded before getting the boot.
And with the Eagle's bolstering an 8.16 team earned run average coming into Wednesday's contest, UK looked to be in great shape.
But Morehead reliever Matt Clark quickly settled in on the mound and seized control of the game. Clark, who carried a 12.56 ERA into Cliff Hagan Stadium, completed six and one third innings while giving up just three earned runs against the Cats.
After thunderstorms halted play for an hour and 27 minutes in the third inning, Clark returned to the mound and continued to pitch.
Starting in right field for the third game this season, Carroll hit an RBI-single in the second inning. First baseman Matt McKinney plated another run with an RBI-single in the fifth inning that gave UK a 5-2 lead.
Morehead cut the lead down to 5-3 and loaded the bases for Hanna in the sixth inning. Hanna ripped a bases-clearing triple off of reliever Brock Baber to give the Eagles their first lead of the game 6-5.
Carroll's double, an SEC-leading 17th on the season, tied the game in the bottom half, but Morehead's three-run seventh proved to be the decider.
UK loaded the bases in the eighth inning for pinch hitter Antone DeJesus. DeJesus was hit in the arm by a 1-1 pitch, but home plate umpire Don Hudson ruled that DeJesus leaned into the pitch and directed him back into the batters box. Antone would ground out to the first baseman to end the Cats' scoring threat.
Thunderstorms delayed play for 45 more minutes before the start of an undramatic ninth inning.
Carroll finished 2-for-5 with two RBIs. McKinney went 2-for-3 while walking once and driving in two runs.
McKinney admitted the team was not playing its best baseball, but declined to go so far as to pinpoint a cause for that.
"It's not just one thing, it's a lot of things right now," McKinney said. "We just have to use practice to try and get it figure it out and take it into the games this weekend. Hopefully we can do that."
UK freshman Tyler Henry made his first official start in a UK uniform. He gave up two hits and an earned run in two innings of work. Brock Baber was charged with the loss after giving up three runs in one and two thirds innings.
The Cats return to action with a weekend series against Florida in Gainsville. The first game is scheduled for Friday at 6:30 p.m.
Antone DeJesus was left out of Wednesday's lineup. The move snapped the UK centerfielder's streak of 68 consecutive games started.
Although technically freshman Tyler Howe was making his first career start against Morehead State on Wednesday, he started the Cats' April 3 game against Western Carolina. However, when the game was cancelled in the third inning because of rain, the records of the contest became void.
Keenan Wiley's 4-for-5 day at the plate raised his season batting average from .269 to .417.
Since UK's series against LSU, which ended on March 25, inclement weather has either delayed or cancelled six of the Cats' games.