Khaldi curled in a superb shot from outside the box 10 minutes into the second half, having set up an early goal for Zakaria Draoui, as USM claimed the trophy for the second time after their maiden success in 2023.
Saadi Radouani also found the back of the net for the visitors, while Iqraam Rayners' first-half penalty for Sundowns proved a consolation.
Sundowns won the CAF Champions League last season to earn their place in the Super Cup this term, but were knocked out before the group stage this time round. USM claimed the CAF Confederation Cup in the 2025/26 campaign.
Sundowns lost Nuno Santos to a knee injury in the warm-up, with Cassius Mailula replacing him in the starting XI, and then lost lead forward Brayan Leon 15 minutes into the game to a groin injury in a double attacking blow for the home side.
USM Alger took an early lead through Draoui and, from a Sundowns perspective, it was far too easy.
Khaldi broke down the right and easily beat Sundowns defender Khulumani Ndamane. His low cross was missed at the near post but turned home from six yards by Draoui.
Sundowns were awarded a penalty when Aubrey Modiba's cross struck the outstretched arm of USM defender Achref Abada. Rayners stepped up to convert in the 25th minute and make the score 1-1.
Thapelo Morena steered a header on target from Mailula's cross and forced a good save from USM goalkeeper Oussama Benbot, who dived low to his right.
Sundowns looked vulnerable every time USM attacked and they went behind again in the 37th minute.
Ndamane could only steer the ball from a corner towards his own goal and when it came back off the crossbar, USM defender Radouani reacted quickest to head into the net.It was the first time Sundowns had conceded twice in the first half of a home CAF fixture for five years, since a 2-0 loss to another Algerian side, CR Belouizdad.
Morena missed an excellent chance to equalise when he scooped the ball over the crossbar from six yards.
The restart of the second half was delayed by around 35 minutes due to the threat of lightning and a heavy downpour.
USM extended their advantage in the 55th minute with a superb third goal as Khaldi picked up the ball on the right wing, cut inside and curled an excellent shot into the far corner of the net, beating the despairing dive of Williams.
Sundowns had plenty of possession but were struggling to create clear-cut chances, and the next goal almost came at the other end as Khaldi tested Williams again, but this time the goalkeeper saved to his right.