Man of the Match Lebese ignited a dull contest with fine strikes at the death at Soccer City.
Chiefs, who beat SuperSport in last year's final, dominated possession and threatened first, as Tefu Mashamaite headed a Siphiwe Tshabalala corner just wide on eight minutes after Kingston Nkhatha stretched Edwin Gyimah down the left flank.
Tshabalala tried his luck in the 23rd minute but his low shot on the angle was comfortably dealt with by goalkeeper Ronwen Williams.
Around the half-hour mark, United striker Bradley Grobler directed a header on goal off a long throw-in but Itumeleng Khune was well positioned to gather.
Grobler then flashed an effort wide of the target from range moments before the interval.
The second period was also short of goal-mouth action, although the fans made their presence felt in the 53rd minute when ex-Amakhosi star Jabu Mahhlangu replaced Morne Nel for Matsatsantsa.
United then suffered a setback in the 80th minute, as Thabo Moloi picked up a knock but was forced to carry on as coach Cavin Johnson had already made three substitutions.
The match looked to be destined for extra-time, especially when Lebese was brilliantly foiled by Williams in a one-on-one situation with two minutes to go.
However, Lebese made amends in the 90th minute with a quality first-time shot in the box following Bernard Parker's cut-back from the right.
Lebese added a second, this time with his favoured left foot in the 94th minute, as he rattled in a Tshabalala pass after arriving late in the area.