Mduduzi Mdantsane opened the scoring for Bakgaga in the seventh minute with a low-left footed shot that squeezed in at the near post, 1-0.
Lucky Nguzana had a chance to double the lead in the 15th minute after being given space inside the box, but his effort went over the bar.
Kgoloko Thobejane was forced into an early change in the 25th minute as Nguzana had a muscle strain on his thigh and was replaced by Rethabile Soso.
The home side started to camp in their own half after 35 minutes and gave Usuthu time and space on the ball.
Cavin Johnson's charges could not do anything positive about their possession and Thobejane's troops went into the halftime break leading 1-0.
Johnson made his first change at the beginning of the second half by withdrawing Somila Ntsundwana for Rhulani Manzini.
Bakgaga also made a change in their striking force as Gift Motupa came on for Robin Ngalande.
The two sides were struggling to keep possession after the hour-mark which reduced the tie to a scrappy affair.
Siyabonga Nomvethe was introduced with 20 minutes left to play in place of Thembela Sikhakhane as Usuthu pushed for an equaliser.
With 10 minutes to play, Motupa made it 2-0 after bull-dozing past his marker and racing clear on goal to score with a low strike.
Bakgaga were threatening to score more goals in the last 10 minutes but their finishing let them down although the three points were already secured.