Maluleka buried an 18th minute effort, before second-half replacement Vuyo Mantjie doubled the visitors’ advantage seven minutes from the end.
Following two wins over Botswana last week, the young South Africans found the going tougher against Lesotho, who host Amajimbos in a second friendly encounter in Maseru on Sunday.
Coach Molefi Ntseki made a hosts of changes to his starting line-up, handing several fringe players an opportunity to impress before finalising his 18-man squad for the 2015 African Youth Championship qualifier against Tanzania next week.
Among those getting a run was midfielder Athenkosi Dlala, who arrived in camp on Wednesday, following family commitments.
Lesotho piled on the pressure and Ntseki made a number of substitutions late in the second period — one of them, Mantjie, who netted in the 83rd minute, to all but secure the result.