Van der Burgh looked relaxed through his 200m breaststroke race, touching the wall quickest in a time of 2:19.44, the third fastest overall behind Ayrton Sweeney (2:18.25) and Jarred Crous (2:19.34).
The Olympic champion will be hoping to go quicker in the semifinals or finals in a bid to dip under the Qualification Time Standards (QTS) for the Fina World Long Course Championships in Kazan later this year.
He has already posted a qualification time in the 100m breaststroke. All participants at the April 13-18 nationals must meet stringent qualifying times set by Swimming South Africa in order to have a chance of making the team that will travel to Russia.
Le Clos, meanwhile, who has uncharacteristically had an off-colour week, continued the trend by coming in fifth fastest in the 100m butterfly heats in a time of 55.38.
George du Rand (53.72) lead the way with the fastest time in that discipline.
In other heats on the penultimate morning, Martin Binedell was the fastest qualifier in the 200m backstroke following a time of 2:04.92.
Luke Pendock was in fine form in the 50m freestyle, topping the qualifiers in a time of 22.90, just ahead of Roland Schoeman (22.94).
QTS times continued to elude the women, and in particular Karin Prinsloo. South Africa’s top female swimmer was the fastest in the 100m freestyle qualifiers, posting a time of 56.74.
Fellow Northern Tigers’ team-mates, Vanessa Mohr (27.04) and Franko Jonker (2:31.33) were the quickest through the 50m butterfly and 200m breaststroke respectively.