Second-half substitute Alex MacDonald drilled home an angled shot on his 24th birthday, after Ivan Toney had fired the Cobblers in front with a 25-yard free kick in the first half that bounced just in front of keeper Jamie Ashdown.
Wilder said: “I thought our performance was excellent, on a terrible pitch. And I thought we controlled possession, so for us to concede in the 90th minute is hard to take.
“My left-back took a chance with a header and he didn’t need to do it. We gifted them the equaliser.
“We were the better side and we were in control. We had the majority of the ball and had the better chances. And i thought we should definitely have been more than one goal up at half-time.
“So to come away with only a point after that is hard to take.”
It was a third successive draw for the U’s, following successive 0-0s against York and AFC Wimbledon.
Oxford head coach Michael Appleton said: “In the first half we were below our normal standards. It just felt a bit flat.
“We were trying to put that right in the half-time team talk.
“And we created more in the first five minutes of the second half than we’d done in the whole of the first.
“We were much better in the second half, and obviously Macca came off the bench and took his goal well.
“I was delighted with the way they stuck at it and made sure they were hard to beat when not playing well.”
U’s goalscorer MacDonald admitted: “We dug in, showed our grit and determination, and hung in there.
“It was a hard-fought point.”
The point made Oxford mathematically safe from relegation, but the two dropped points were a big blow to Northampton’s slim chances of reaching the play-offs.