The Students left the Orlando Stadium encounter empty-handed after goals from Thabo Matlaba and Tlou Segolela handed the Buccaneers the 2-0 win which took them just one point below PSL leaders Kaizer Chiefs.
Speaking after the match Habas paid credit to the Soweto giants, but was left furious with the match official who denied his side what appeared to be a clear penalty when the scores were at 1-0.
"We played fantastic, and Pirates also played fantastic, but the referee cost us," Habas said bluntly.
The result left the Clever Boys seventh in the standings with 16 points from their opening 12 Premiership matches, although they now sit just six points above the relegation zone.