It was the league leaders who opened the scoring, with Craig Tanner hitting home into the bottom corner on fifteen minutes.
The U's own Craig, midfielder Slater, got the equaliser with a superbly struck free-kick just after the half hour mark.
In the second period, the game looked to be heading for a draw until the referee clashed with Spencer in the seventy fifth minute and was down for over ten minutes with a back injury.
Immediately the game resumed, Walker's clearance from a Prosser back pass hit sub Ryan Donaldson and rebounded into the U's net for an unlikely winner.
At the start of the game, the U’s were more than matching their table topping opponents, and it was they who had the first effort at goal.
Drey Wright got in down the right on four minutes, but couldn’t find the target with an angled shot and failed with a half-hearted appeal for a corner.
At the other end, Sam Walker’s first involvement saw him quick off his line to get to the ball ahead of Jimmy Spencer.
Three minutes later, he was picking it out of his net though.
Wright was on the deck having been caught by Carey, and the Plymouth number ten made great use of the space before playing it inside for Craig Tanner to finish smartly into the bottom corner.
On nineteen minutes, Denny Johnstone had his first opening, but mistimed his volley after headed knock-ons from Luke Prosser and Kurtis Guthrie.
Wright was next to trouble the home defence, but Guthrie shot well wide when found by the U’s winger.
There was a scare for the U’s on twenty five minutes, when Walker’s punch hit teammate Chris Porter in the face, rebounding behind for a corner.
Four minutes later, Walker began the spell of pressure that ultimately led to the U’s levelling the scores.
He caught a cross, then instantly launched it into the path of Wright down the right wing.
Wright beat his man and from his cross, Porter couldn’t get the contact needed and the ball was half cleared.
When it came back to Porter on the edge, he was fouled and the ball was placed nineteen yards from goal by Craig Slater.
Slater brilliantly curled his free kick over the wall and into the corner, giving the U’s the equaliser against the table toppers.
A free kick at the other end failed to trouble Walker on thirty six minutes, curling wide of the U’s goal.
Johnstone and Slater both had chances towards the end of an intriguing half, the former volleying at McCormick before the latter shot wide.
The second half started with the U’s on the attack, Wright getting in a shot that didn’t trouble McCormick after good work from Johnstone and Porter.
That came a minute into the half, and Plymouth had their first effort just two minutes later when Slew shot harmlessly wide after a good turn.
The game settled down into a midfield battle, but it was the U’s who were looking more comfortable.
On fifty seven minutes, Kane Vincent-Young mishit a cross and McCormick had to scurry backwards to tip it over his bar.
From the corner, Kurtis Guthrie got to the ball first but his effort clipped the outside of the near post on its way out for a goal kick.
With the home threat having been well stifled, the U’s continued to look the most likely to win it, but any momentum went with a nasty looking injury to the referee.
He collided with Spencer inside the home half and went straight to ground, where he remained as both physios rushed on to assist.
With a spine board immobilising him, he was stretched off and a further official was found to perform fourth official duties.
The long delay affected the U’s, with the home side immediately taking the lead again.
Plymouth got the ball forward from the throw in, and Luke Prosser got there first and elected to pass back to Walker.
Walker always looked favourite to get there but his clearance was charged down by sub Ryan Donaldson, with the ball rebounding past Walker and cruelly into the U’s empty net.
With the official time showing ninety minutes, but only about seventy five played, McGreal made three changes to try and get his side back in the game.
Bonne, Szmodics and Fosu came on, but they couldn’t prevent the U’s falling to defeat.
Bonne did have a late volley saved, but it looked like he was impeded but tried to stay on his feet to get the shot away.
It was a cruel way for the U’s to lose the game, after more than matching the team at the top of the league two table.
Their thoughts now turn to the FA Cup First Round tie against Chesterfield next weekend.