The Arrows goals were scored by Norman Smith (pictured) and Musa Bilankulu while Destin Makita scored for Pirates.
The home side played well and did have the better scoring opportunities particularly during the first half.
The Prates fans misbehaved and started throwing various objects onto the field after Arrows took the lead late in the game.
Fans were calling for the axing of coach Bibey Mutombo and he needed to be escorted out of the stadium in a police car while fans threw stones at police.
This is Pirates’ third loss in four League games.
In the 14th minute Pirates nearly scored when Destin Makita headed wide of the post.
Arrows came close when Kagiso Senamela hammered his shot narrowly over the bar in the 25th minute.
Kagiso Dikgacoi had a chance but hammered his shot straight at keeper Francis Chansa.
Pirates scored in the 53rd minute when Makita got a boot to the ball after a goalmouth scramble to give his side the lead.
In the 58th minute Arrows equalised when Norman Smith receiving the ball from the left and turned Makita to score with a left-footed shot giving Chansa no chance.
Lebohang Mokoena had his shot well saved by keeper Brendon Wardle in the 62nd minute.
Bennett Chenene came very close to giving Pirates the lead in the 67th minute, his shot hitting the upright.
In the 83rd minute Arrows took the lead when Musa Bilankulu scored with a header from a corner.