James Constable, Deane Smalley and Sean Rigg were on target as Oxford ran out 3-0 winners on the final day, while Lee Molyneux saw red for Stanley in the 89th minute.
"We are disappointed as we wanted to finish with a win but I can't be too negative as the players have been fantastic," said the Stanley manager, whose side were bottom of the League Two table at one point but one defeat in eight prior this reverse secured their survival.
"Perhaps this was a game too far but I have got to give the players credit and it's nothing short of a minor miracle what they have done.
"I have started having conversations with the players now about contracts for next season.
"We will be trying to keep the nucleus of the squad together and then build from there."