Thabo Mnyamane opened the scoring, before Thembinkosi Lorch leveled matters in the 75th minute.
However, Baxter felt his side were denied a clear penalty in the second half when Ayanda Gcaba appeared to have been brought down Jeremy Brockie.
"I thought we were comfortable whole night, I thought the first half they flattered to deceive, apart from linesman, who was probably their best player this evening," Baxter said after the game.
"We go a goal up, we still dominated the game. We had a stick no penalty. We scored a wonderful goal with Jeremy Brockie's timing of movement. and the combination play around the box.
"They don't realise how hard we work with that and someone just wipes that away and then Pirates get back in the game with a set-play, that's poor of us.
"We still had chances in transition. I'm pleased with the way the players have played tonight, Come to Orlando stadium in this time when they are a more healthy club than they were a while. We should have won the game and I feel sorry for them."