The Young Clever Boys triumphed 5-3 on penalties after the teams had played to a thrilling 2-2 draw in the decider, their second title having last won the competition, now in its 10th year, in 2011.
Sundowns took the lead through Tlotlego Pitso but were pegged back when Mbongeni Kanyane equalised for Wits.
Pitso, who finished as tournament top-scorer with six goals, looked to have won the game for Sundowns when he added his second, but Simphiwe Mabena levelled again for Wits, who then held their nerve in the shoot-out.
The four pool winners from the tournament have all qualified for the prestigious Future Champions Gauteng International Tournament that will be staged at the Nike Football Training Centre in Pimville from 19th to 24th March.
There they will join some of the top academy sides in the world and Highlands Park, Sundowns, Orlando Pirates and Wits will seek to become the first South African winners of the top junior competition.
Earlier on Sunday, Wits edged Highlands Park in a tense semi-final fixture that ended 0-0, with The Clever Boys taking the tie 5-4 on penalties.
The other semi-final was equally tight as tournament joint top-scorer Cassius Mailula converted a penalty for Sundowns, but Bongani Monabeng netted for Pirates to take the game to spot-kicks.
But it was Sundowns who came through the shoot-out as Riandre Vries and Tlotiso Ndziwa were the only two players to net their penalties in a 2-0 win for The Brazilians.
Pirates then picked up the bronze medal when they defeated Highlands Park 3-2 on penalties after another 1-1 draw.
Lance Makambi netted for the Young Buccaneers but they were pegged back by a goal from Santino Smith for Highlands Park that took the game to a shoot-out.
The two days of action showed the quality of junior sides in the Gauteng Province and started with the pool stages on Saturday.
Highlands Park qualified from Group A on Saturday with three wins, the decisive victory being a 2-0 success over School of Excellence, who were runners-up in the pool.
Sundowns were in a close run for Group B by both SAFA Johannesburg and SuperSport United but ended top of the pool with two wins and a draw.
The decisive result in the pool was Sundowns’ 2-0 win over SAFA Johannesburg, but they were held to a 1-1 draw by Tshwane rivals SuperSport.
Group C was another tight one, but Pirates edged the pool, with one of their two wins coming against Soweto rivals Kaizer Chiefs as they secured a 1-0 success.
Chiefs, in the end, could only manage third place, with Clapham High School finishing as runners-up in the pool.
Wits stormed through Group D, winning all three of their matches and proving the most prolific side in front of goal in the first round with 13 goals scored and just one conceded.
Jomo Cosmos were runners-up in the pool with two wins but were up against it when they lost their opener to Wits.
There was also a Gauteng Cup women’s competition played for the first time in 2018 between four teams, with the final to be staged as a curtain-raiser to the Future Champions Gauteng International Tournament final on 24th March.
Zara Walker scored a hat-trick as SAFA Johannesburg emphatically booked their place in the decider with an 11-0 win over an Ekurhuleni Invitational side.
They will take on SAFA Tshwane, who were 2-1 winners over SAFA Ekurhuleni as Paballo Chela and Lethabo Ledwaba were on target.
The Future Champions Gauteng tournament is organised by Global Sports International in conjunction with Gauteng’s Department of Sport, Arts, Culture and Recreation, and Department of Education, as well as the South African Football Association.
Other sponsors include Clinix, Sedgars Sport, LaLiga and Gauteng Coaches.
RESULTS AND TABLES
SAFA Tshwane 1-4 Highlands Park
SAFA Ekurhuleni 0-1 School of Excellence
SAFA Tshwane 0-1 SAFA Ekurhuleni
Highlands Park 2-0 School of Excellence
SAFA Tshwane 2-2 School of Excellence
Highlands Park 3-1 SAFA Ekurhuleni
P W D L GF GA PTS
Highlands Park 3 3 0 0 9 2 9
School of Excellence 3 1 1 1 3 4 4
SAFA Ekurhuleni 3 1 0 2 2 4 3
SAFA Tshwane 3 0 1 2 3 7 1
Mamelodi Sundowns 1-1 SuperSport United
SAFA Johannesburg 2-0 Fumana High School
Mamelodi Sundowns 3-0 SAFA Johannesburg
SuperSport United 4-1 Fumana High School
Mamelodi Sundowns 8-0 Fumana High School
SuperSport United 1-2 SAFA Johannesburg
P W D L GF GA PTS
Mamelodi Sundowns 3 2 1 0 12 1 7
SAFA Johannesburg 3 2 0 1 4 4 6
SuperSport United 3 1 1 1 6 4 4
Fumana High School 3 0 0 3 1 14 0
Orlando Pirates 1-0 Kaizer Chiefs
SAFA Sedibeng 1-1 Clapham High School
Orlando Pirates 3-0 SAFA Sedibeng
Kaizer Chiefs 2-2 Clapham High School
Orlando Pirates 0-3 Clapham High School
Kaizer Chiefs 2-1 SAFA Sedibeng
P W D L GF GA PTS
Orlando Pirates 3 2 0 1 4 3 6
Clapham High School 3 1 2 0 6 3 5
Kaizer Chiefs 3 1 1 1 4 4 4
SAFA Sedibeng 3 0 1 2 2 6 1
Bidvest Wits 2-1 Jomo Cosmos
SAFA Westrand 2-1 Rosina Sedibane Sports School
Bidvest Wits 6-0 SAFA Westrand
Jomo Cosmos 2-0 Rosina Sedibane Sports School
Bidvest Wits 5-0 Rosina Sedibane Sports School
Jomo Cosmos 6-0 SAFA Westrand
P W D L GF GA PTS
Bidvest Wits 3 3 0 0 13 1 9
Jomo Cosmos 3 2 0 1 9 2 6
SAFA Westrand 3 1 0 2 2 13 3
Rosina Sedibane 3 0 0 3 1 9 0
Highlands Park 0-0 Bidvest Wits (Wits won 5-4 on pens)
Mamelodi Sundowns 1-1 Orlando Pirates (Sundowns won 2-0 on pens)
Highlands Park 1-1 Orlando Pirates (Pirates won 3-2 on penalties)
Bidvest Wits 2-2 Mamelodi Sundowns (Wits won 5-3 on penalties)
6 goals – Tlotlego Pitso (Mamelodi Sundowns)
4 – Cassius Mailula (Mamelodi Sundowns)
3 – Zuko Gxabuza (Jomo Cosmos), Leo Mert (Bidvest Wits), Siyamamkela Ntame (Highlands Park), Sindiswa Zondi (Jomo Cosmos)
2 – Nzeeocha Chinedu (Kaizer Chiefs), Thato Mabunda (Clapham High), Brian Makgabathe (Safa-Tshwane), Bongani Monabeng (Orlando Pirates), Thulani Ngonyama (Supersport United), Bennett Razeen (Supersport United), Ntsakiso Shiburi (Jomo Cosmos), Andile Simelani (Bidvest Wits), Santino Smith (Highlands Park), Riandre Vries (Mamelodi Sundowns)