The midfielder was selected by South Africa for an eight-nation Olympic Games qualifying tournament in the Egyptian capital, which kicked off Friday.
Fellow SuperSport midfielders Teboho Mokoena and Athenkosi Dlala were also chosen for the national under-23 squad, and the trio will miss the opening match against Zambia Saturday.
Mbule played the entire match against Wits, Mokoena was substituted late in the second half, and Dlala did not make the 18-man matchday squad.
The refusal of SuperSport and several other clubs to release players outside the November 11-19 international window infuriated former South Africa great Neil Tovey.
"It is a disgrace. It is downright diabolical that they cannot have the best players," said Tovey, who captained hosts South Africa to the 1996 Africa Cup of Nations title.
After coaching several local top-flight clubs, Tovey is now the South African Football Association technical director.
SuperSport and Wits swapped places with the Pretoria outfit rising to third after a fortunate win as the home side dominated only to fail as Mbule nodded into the corner on 91 minutes.
Kaizer Chiefs top the table with 25 points as they seek a first league title in five seasons, defending champions Mamelodi Sundowns have 18, SuperSport 17 and Wits 15.
'Heart and effort'
"This match was not about tactics -- it was about heart and effort," said SuperSport coach and former Zimbabwe captain Kaitano Tembo.
"The longer the match remained goalless, the greater the chance that we would steal maximum points."
After slamming six goals past Mozambican visitors UD Songo in the CAF Confederation Cup last Sunday, Wits coach Gavin Hunt lamented his side not being able to net even once.
"Gift (Motupa) scored four last weekend and could have had six tonight. Had we scored early, I believe we would have won by at least four goals."
Elsewhere, Maritzburg United came from two goals behind at home with four minutes of regular time remaining to draw 2-2 against Bloemfontein Celtic in a mid-table clash.
Goals from Lesotho international Sera Motebang and Siphelele Luthuli put Celtic in a strong position to take three points away from eastern city Pietermaritzburg.
But Daylon Claasen converted a United penalty to restore hope and another substitute, Judas Moseamedi, levelled in the third minute of stoppage time.
Each side climbed two places after the dramatic climax -- Celtic to seventh and Maritzburg to eighth.
The highlight of the seven-match weekend Premiership schedule is on Saturday when Chiefs will face ninth-place Orlando Pirates in a Soweto derby expected to be watched by an 85,000 crowd.