The officials were heavily involved in dictating the outcome of the tie, sending off three players and three technical team members.
Lerato Lamola and Kudakwashe Mahachi scored either side of a red card shown to Wits' new signing Damjanovic before James Keene scored from the spot to reduce the arrears and Danny Phiri was sent off just before the half-time whistle.
In the second stanza Keene grabbed the leveller to take the game past the 90 minutes and into extra-time, where Siyabonga Dube was shown red for violent conduct, before proceedings were eventually settled on penalties with Wits walking away 4-3 victors in the shootout.
The hosts looked threatening from the onset and Vincent's Pule's whipped cross almost snuck in at the far post despite a stretching James Keene failing to make contact.
Moments later Wits almost had the ball in the back of the net as Thulani Hlatshwayo rose to head towards goal only to see his effort scrambled off the line.
As the game moved past the 10 minute mark Arrows struck completely against the run of play as a simply delightful cross from Siphelele Magubane allowed Lamola to steer his header home.
Siyabonga Dube warmed the palms of Moeneeb Josephs in the 16th minute with a seering drive from range as Arrows grew in confidence.
Wits' task was made more difficult in the 22nd minute as debutant Damnjanovic made an ignominious departure after being shown a red card for a horrific high boot challenge that rendered Magubane unconcious.
Abafana Bes'thende capitalised on their man advantage almost instantly with Wayde Jooste feeding Mahachi who slotted home from close range although he looked to be offisde.
At the other end Arrows failed to keep their cool and a rash challenge from Nkanyiso Mngwengwe on Vincent Pule afforded Wits a chance from 12 yards.
Keene took on the responsibility of converting the penalty and dutifully did so, dispatching the spot kick into the top right corner.
Moments before the end of the first stanza Phiri was given his marching orders as the referee produced a second yellow card for the Zimbabwean.
Wits put pressure on their visitors after coming out from the break but Arrows did a decent job of keeping them at bay with Pule resigned to having a go from distance.
Just before the hour mark the winger had an opportunity from closer range but was crowded out as he tried to pull the trigger from a tight angle.
The hosts endeavours were eventually rewarded in the 62nd minute as Lehlohonolo Nonyane tried to touch the ball back to Nkosingiphile Gumede via his chest but Reeve Frosler nipped in and lifted the ball towards goal for Keene to slide in for his second.
Hlatshwayo then put his header wide at the back post under pressure from Nonyane as the game opened up.
Seconds after entering the fray Gabadinho Mhango had his header cleared off the line whilst at the other end Nonyane tested Josephs at his near post.
Daylon Claasen smashed the ball goalwards on the half volley inside the final ten minutes only to see it crash off Nonyane's arm but Phillip Tinyani was unmoved by the appeals.
With regulation time winding down Mhango's cross was not well held by Gumede and Frosler stabbed home only for the official to rule it out despite the goalkeeper not having control of the ball.
In the first period of extra-time Mhango laid the ball square to substitute Steve Pienaar who lashed an effort just over the crossbar on his Wits debut.
At the other end Mahachi smashed a first time effort just wide of the upright with Josephs rooted to the spot.
The drama intensified as referee Tinyani, upon instructions from fourth official Victory Hlungwani, sent Wits coach Hunt and Arrows duo Clinton Larsen and Mandla Ncikazi to the stands for verbal abuse.
Josephs was made to work moments into the second-half of extra-time as he palmed away Sibiya's curling effort.
The game finally boiled over as Dube, having been fouled by Mhango, headbutted the Malawian and received a red card which resulted in a brief fracas between the two outfits.
The game needed to be settled on penalties and despite missing their first two spot kicks, Wits triumphed by a scoreline of 4-3.