Substitute Dean Morgan poked the ball home in stoppage time for what he thought was a vital winner in this battle at the bottom of League Two, but it was disallowed.
"We had a goal disallowed for offside right at the end but it was a goal, it's legitimate which is why it is hard for us to take," said Ainsworth, whose side remain out of the relegation zone on goal difference.
"These officials have got to be better at this level. Looking at the replay there was no offside, it is a totally legitimate goal. The linesman has cost us a couple of points that could be huge come the end of the year.
"The linesman said Dean Morgan was offside but he is not offside, he is onside but we have to take it. I'm expecting a lot of decisions to go our way in the final three games now.
"I'm really proud and pleased. I thought we played the better football. It wasn't a must-win game, it was a must-not-get-beat game and we didn't get beat.
"I think we had the better of the game, if it were a boxing match we would have won on points."
Northampton have been in the bottom two since September but temporarily edged out when Ricky Ravenhill's speculative effort from distance, combined with an error by home goalkeeper Matt Ingram who was later credited with the goal, saw them take the lead.
But on 18 minutes Wycombe were level. Aaron Pierre headed across goal into the corner of the net from Matt Bloomfield's free-kick after a foul by John Marquis.
The result leaves both sides locked together with Bristol Rovers on 47 points with just three games remaining.