Having lost 1-0 in the first leg a fortnight ago at Eldorado Park, the Amajimbos exited the competition 3-1 on aggregate, barely a week after their seniors, Bafana Bafana, missed out on a 2010 Africa Cup of Nations finals place in Angola.
Played in a strong wind, Amajimbos took the game to the hosts and pinning the Malawians in their half, though defender Zenzele Zungu had to clear a Malawian goal-bound shot off his line against the run of play.
Chief culprits for the visitors were strikers Andile Khena and Thabiso Khwela, who wasted a number of glorious opportunities, as they had in the first leg.
Instead, it was Malawi who went in front as diminutive midfielder Tony Chitsulo beat Mbongeni Gumede with a stunning 40-metre dipping shot in the 39th minute.
The goal took the steam out of the visitors and they conceded a second goal that all-but sealed the tie just before halftime as a defensive mix-up gave lurking striker Andy Simukonda the opportunity to fire a low shot into the net.
The South Africans came out for the second half firing on all cylinders, especially after the introduction of slippery winger Thomas Serubarube, but once again poor finishing, and to some extent the hosts steely defending, contrived to deny the Amajimbos a goal.
But finally the visitors got a consolation on the dot of fulltime when Lebohang Maloto scrambling the ball into the net from a rebound, two minutes after Andile Khena's well-executed close-range shot had bounced off the upright.
The African Youth Championship finals will be played in Algeria, starting on March 19, 2009.
By Peter Kanjere in Blantyre