Matty McNeil lashed home to give the hosts hope after 79 minutes, then four minutes later Oli Johnson levelled it up after his shot flew in via a deflection off the unlucky Tony Craig.
Jackett said: "I was hopeful after the penalty put us two up, but you should never think a game is over when you're up against a side with as much size and presence as Stockport.
"Even when we went down to 10 men you'd still have to be looking for us to come through the situation and gain the victory.
"I'm frustrated, but there's a lot of games left and it's up to me to continue to try and find the right equation on the pitch. I still have every confidence in my lads to go on a run that will get us promotion."