Jeff Goulding came off the bench to grab an 87th-minute winner, in a thrilling game at the EBB stadium, after the Shots threw away a two-goal lead.
Paul McCallum gave Aldershot a controversial lead when the linesman confirmed he had bundled Craig Reid's cross over the line despite Damien Batt's attempted clearance.
Reid doubled the lead from the spot but Scott Davis and Jon-Paul Pittman drew Oxford level either side of Michael Raynes' red card. But the Shots hit back through Goulding.
"I think it's difficult for the linesman to see, unless she is unbelievably sure, which she said she was," the Oxford boss said.
"I'm a bit perplexed how she can be so clear and sure on the decision. We lost Micheal Raynes but all we've done is given them an opportunity to win the game with the free-kick.
"It's knocked the stuffing out of everyone. The decisions that the players were making absolutely killed us and put us on the back foot.
"We aren't in the position we want to be and I understand that. We aren't fighting for our lives though, we've got four games to go and people need to assess at the end of those games.
"I know there are murmurs and rumblings but I'm not walking away from anything."