Preston took the lead through skipper Sean St Ledger as he glanced home a near-post header from Ross Wallace's 18th-minute corner from the right.
Argyle levelled from a 70th-minute spot-kick converted by midfielder Damien Johnson.
The penalty was awarded after the ball hit midfielder Matt James' hand as he attempted to clear Carl Fletcher's header towards goal, following a corner from the left by Argyle substitute Craig Noone.
Preston had dominated the early exchanges.
Stockdale made a brilliant 12th-minute block to deny James from six yards while Wallace fired just over after 25 seconds as the Lilywhites took the game to their hosts.
Wallace's 30-yard free-kick was palmed out by home keeper David Stockdale and Republic of Ireland central defender St Ledger's first-time strike flew just past the post.
Ferguson said: "The game should have been over after half an hour, we absolutely battered them and had plenty of chances.
"I felt we played really, really well in the opening period of the game.
"We knew Plymouth would come out battling and I thought my lads stood up to them really well and it's taken a penalty for them to get back into it.
"They had a lot more pressure in the second half but my players' effort and determination to try and win the game was magnificent again.
"I just feel if we had taken our chances we win the game."
In the 89th minute Noone crashed a 25-yard drive off the bar only for North End number one Andy Lonergan to brilliantly save Rory Fallon's diving header follow-up.
Lonergan also made a spectacular save at the end of the first half, twisting to palm over rookie striker Joe Mason's header from Chris Clark's cross as Argyle began to claw their way back into the game.
Argyle head coach Paul Mariner said: "Some people are saying it was the tale of two halves but I think it was a tale of a third and two thirds.
"For the first 30 minutes we weren't at the races at all and Preston could have been out of sight. Luckily they weren't and in the end we could have won it.
"I thought their goalkeeper Lonergan had a fantastic match for them and (Youl) Malwene and St Ledger defended resolutely, and they had to.
"We just have to be a little bit more clinical in front of goal, every manager says it.
"It's good that we are creating chances but we didn't get enough balls into the final third in the first 30 minutes. In the final 60 minutes we did everything bar put the ball in the net again."