The ball boy was ordered to leave the pitch deep in stoppage time after throwing a reserve ball on to the pitch because he believed the match ball had trickled wide when it was still in play.
It was the second time the referee had flashed a straight red card at Soccer City, dismissing Chiefs defender Sibusiso Khumalo for a high, late first-half tackle.
The match official was the centre of attention again in first-half stoppage time when he ignored Cape Town appeals for a goal.
Chiefs goalkeeper Itumeleng Khune palmed away a Sibusiso Masina header, but big-screen replays showed the ball crossing the goal-line before being cleared.
Mitchell Katsvairo put Chiefs ahead after three minutes, deflecting a George Maluleka drive past goalkeeper Shu-Aib Walters from close range.
@KaizerChiefs _ Was it really necessary for Gomez to humiliate the young ball boy like that, a small talk would have been the best option— Thabo Victor (@Sovicta) November 29, 2016
Another deflection gave City a 53rd-minute equaliser as a shot by Matthew Sim struck an outstretched leg of Lorenzo Gordinho and spun over Khune into the net.
City coach Eric Tinkler was unhappy despite taking a one-point lead over Wits at the top of the 16-club table.
"It was a very frustrating match for me," he told reporters. "When we had a one-man advantage, the plan was to move the ball wide, stretch Chiefs and create space.
"However, we constantly attacked down the middle, making it easier for our opponents to survive second-half pressure.
"We were extremely lethargic during the opening half and we committed a comedy of errors during the second half. I feel we lost two points rather than gained one."
The draw ended a run of seven victories in all competitions for City.
Cape Town City have 21 points after 11 rounds, SuperSport United and Wits 20 each, Chiefs and Golden Arrows 17 apiece and Orlando Pirates 16.
SuperSport scored twice within seven minutes during the second half to win 2-0 against Wits in Nelspruit and inflict a first league defeat this season on the Johannesburg club.
That Kaizer Chiefs ball boy did that on purpose. He knew what he was doing.— Macdonald Thobang (@Macd_Thobang) November 29, 2016
Clayton Daniels bundled the ball into the net on 64 minutes after a corner and Thabo Mnyamane scored direct from a free-kick at Mbombela Stadium.
Mid-table sides Maritzburg United and Chippa United drew 1-1 in the other Premiership match and five more fixtures are scheduled for Wednesday.
Original source: Chiefs ball boy given a red card