The Buccaneers looked home and dry after a dominant start that saw them score two brilliant goals through Linda Mntambo and Kabelo Dlamini.
Pirates were 2-0 up in the 80th minute with maximum points in the bag.
But the wheels came off, starting with a Happy Jele own goal and then a last-minute strike from Gerald Phiri Jr stunned the Sea Robbers to give Baroka a massive point.
“You don’t remember the goals and the type of football we played when the results end like this,” Mokwena said.
“There was one team on the pitch to be honest, until it was 2-1 and we showed psychological frailties. It is what it is.
“When it was 2-0, I thought that it was going to be 3-0.
“(Vincent) Pule had a good chance.
“(Gabadinho) Mhango had a good chance to make it three, four. It’s definitely two points dropped.”
Pirates have just won four matches out of the 13 they have played in the Absa Premiership. It’s a disappointing return for a team that was expected to fight for the championship at the start of the season.
But their inner turmoil, started by the shock resignation of coach Micho Sredojevic, derailed those plans as the club was put in a tailspin.
Mokwena has tried to steady the ship, but inconsistency has been Pirates’ downfall.
The club would produce a good performance or get an important win, only to go two steps back in their next encounter. It’s a situation that has frustrated the Ghost to a point that they voiced their displeasure towards the club at the Peter Mokaba Stadium after the match.
“I don’t control that (fans’ reaction),” Mokwena said. “I can’t speak about the fans. I speak about what we can do.
“What we can do is to try and do our best all the time. The Pirates fans know that if there is one thing about us, we give it our best for the badge, we fight for the badge.
“We spoke about our inconsistency. We are struggling to be a bit more consistent and pull through with two matches.
“We will work on it and we just keep going.”
Mokwena has his work cut out for him if he is to win over the supporters and take the club back to where it belongs having finished second on two occasions in the last two seasons.
While they struggle, their rivals Kaizer Chiefs have been blowing away competition which has heightened their problems. Pirates’ last game of the year will be against Black Leopards at Orlando Stadium on December 21.
They can’t afford to slip-up in that match like they did against Leopards’ Limpopo neighbours.
“It’s disappointing, it feels more like a defeat to be honest because you were leading 2-0. Disappointing! Obviously, we made a couple of mistakes, dealing with the throw-ins,” Mokwena said.
“If you concede two goals, you can’t say that you don’t have defensive issues especially the way we conceded the goals. It is what it is, unfortunately we conceded two.”