The 2004 Athens gold medallist clocked 49.38 seconds to secure the fastest time en route to the semi-finals.
Townsend, one of 12 swimmers at this week's meet who have already set 'A'-standard qualifying times for the Games, missed out on booking his ticket to London on Wednesday night when he was fractionally outside the required time in the 200m freestyle, despite winning the title.
The qualifying criteria requires all the country's Olympic hopefuls to swim below the standards twice during a 10-month period, including once this week.
The 27-year-old, who also has an 'A'-standard time in his main 200m individual medley event, looked at ease in the morning heats as he ended ahead of Gideon Louw (50.03) and Graeme Moore (50.18).
Moore, the only one of the three with a qualifying time already under his belt in the event, was making his first appearance of the championships.
Roland Schoeman, another former Olympic champion, qualified fifth quickest in 50.75.
Elsewhere, Mandy Loots was the fastest in the 200m butterfly heats with a time of 2:13.21.
Loots, who has yet to qualify for London and missed her other chance to get there via the 100m butterfly, was much faster than second-placed Jessica Pengelly (2:17.93) and Bianca Meyer (2:19.69) in the longer event.