Play-off outsiders Oxford had won their last three games on the road but Ben Harding grabbed the crucial winner as Cobblers maintained their promotion push with a ninth straight home success.
U's boss Wilder said: "I'm disappointed not to be going away with all three points let alone one. I don't think we deserved to get beaten, especially based on our second-half performance.
"But, as has been the case all season, we've not done it in the final third. We got into some great positions in the second half and I also thought we had the better chances in the first half.
"But we conceded more than two minutes into first-half stoppage time, Andy Whing got took about by Clive Platt and before we know the ball is in the back of the net.
"We gave it a right go in the second half but for the second week running we've not punished teams. We need players to be brave enough to take a chance.
"We kept going right to the end and that's what we'll do right to the end of the season but we know we've got to win a lot of games now to get into the play-offs. Northampton are a very strong side, especially at home, and we pushed them all the way."