Lee Miller's headed effort was ruled out by Salisbury, who said the on-loan Middlesbrough forward Lee Miller had fouled Greg Halford while challenging for the ball.
Baraclough spoke to the referee after the game, even asking him to review video footage of the goal.
"He said he's not supposed to look at things like that and I don't know why. We're not allowed to show him footage for some reason," he said.
"The referee has stood by his decision, said he was climbing all over the back of him. The referee was the one who gave the decision, but the reaction of all 22 players told you it was a goal. I've tried to show him the footage and he's nowhere near Halford when he leapt and attacked the ball."
Baraclough made five changes to his starting line-up for the game after a disappointing performance at Bristol City on Saturday, and felt the players who came in had helped his side compete against a team that had won their last four Championship outings going into the game.
"For long spells, especially the first half and the beginning of the second, I thought we were the better side. If we went in at half time 1-0 up, how it should have been, then I think it would have been a different game," he added.
"We limited them in the first-half, we passed the ball well on a good surface. The game plan was working perfectly. They upped the tempo and we had to match them.
"They still weren't creating great openings but the first goal gave them a bit of belief. As they stepped up a gear we weren't able to match them. We've got to be strong enough mentally to cope with that."
Steve Cotterill, the Portsmouth coach, praised his side's attitude. At the start of the season Pompey's well-documented financial problems led to many tipping them for a second successive relegation.
"I'm sure there will be a lot of teams equally as big as us who would give their right arm to be where we are," he said.
"All credit to the lads - they've kept their heads down and carried on working. Hopefully they're getting a few rewards now."