First half goals from Velemseni Ndwandwe and Thembela Sikhakhane and a second half strike from Magubane saw Abafana Bes'thende to victory.
Right from the onset Arrows were in the ascendency as Sibusiso Sibeko combined with Quincy Ngcobo before forcing the keeper into making an excellent stop.
The pressure did not abate and the PSL side eventually broke the deadlock with Sibeko putting the ball on a platter for Ndwandwe to head home.
Uthukela did their best to find a way back and enjoyed a decent spell but Arrows went into the break with a two goal advantage as Sikhakhane squeezed the ball into the net following a good long ball from Veluyeke Zulu.
The visiting team were put under no real pressure in the second period and with victory all but assured they made a host of substitutions, making sure that plenty of players got a run-out.
Amongst those substitutions were Seth Parusnath and Magubane who combined brilliantly for the latter to score close to the end of proceedings as Arrows followed up their 1-0 win over Free State Stars with a victory in the final.