Cape Town - Kgokolo Thobejane's side were searching for their first league home win of the season and they made a good start by creating two early chances.
Albert Mothupa dragged his shot wide of the right post in the fourth minute after being teed up by Marshall Munetsi inside the area, before Geoffrey Massa forced Jackson Mabokgwane into a save at his near post three minutes later after Siphelele Zikalala's initial effort had been blocked.
Mothupa then headed the resulting corner wide of the left post, and Pirates were soon threatening when Tendai Ndoro was played through on goal by Mpho Makola but after rounding Oscarine Masuluke, the striker could only find the side-netting from a narrow angle on the right.
However, Bakgaga were on the attack again moments later as Dineo Shaku was allowed to carry the ball all the way into the area from inside his own half before feeding Richard Matloga, who draw a save out of Mabokgwane on 10 minutes.
Munetsi then failed to hit the target from inside the area after connecting with Tshepiso Lietsisa's cross from the left, while Soso Rethabile curled a shot wide of the right post from 22 yards out on the quarter-hour mark after dispossessing Issa Sarr.
Mabokgwane had to be alert to cut out a through-ball meant for Rethabile in the 25th minute as the keeper came racing off his line to make the interception.
Ndoro was presented with another opportunity for the visitors three minutes later after being played through on goal on the left, but he fired wide of the left post from seven yards out under pressure from the defender.
The final chance of the first half saw Rethabile test Mabokgwane from 22 yards out as the two teams went into the break at level pegging.
However, the deadlock was broken just three minutes into the second half when Chabalala slotted home at the back post unmarked after Masuluke was impeded by Sarr from a corner.
Mzwanele Mahashe then went close to equalising on two occasions before the hour mark as he headed wide from corners - one at the near post and the other at the back post.
Lietsisa tried to catch out Mabokgwane on 62 minutes with a shot from the left flank that he had to push over the crossbar, while Munetsi gave the keeper more work to do six minutes later with a low strike from outside the box.
Baroka continued to push for the equaliser at it came from the most unlikely of sources as Masuluke, who had gone up for a corner deep into stoppage time, netted with an audacious overhead-kick from all of 16 yards out after Mabokgwane had punched the ball clear.