Boland finished the rain-affected day with figures of 4-31 to put Australia in a strong position with South Africa to resume on Tuesday with captain Temba Bavuma 41 not out and Wiaan Mulder unbeaten with two runs.
Play got underway at 3:45 p.m. local time (1345 GMT) with 30.4 overs bowled after heavy rain in the morning threatened to wash out Monday's play.
Boland, who took two wickets in the one hour of play possible on Sunday, added a third in the third over of the second day's play, inducing an edge from debutant opener Marques Ackerman, who was dismissed for six.
Matthew Breetzke, brought into the home line-up after the 214-run defeat in the first test in Durban last week, then departed for four runs after he was also caught behind by wicketkeeper Alex Carey, playing away from his body to Mitchell Starc's left-arm delivery.
South Africa were in a precarious position at 40-4 but Bavuma led a fightback with Ryan Rickelton as they put on 52 runs for the fifth wicket.
Rickelton was dropped on 26 by leg slip Marnus Labuschagne off captain Pat Cummins in what looked a regulation chance, but he only added five more runs before a brilliant one-handed catch by Matt Renshaw at first slip gave Boland a fourth wicket.
Bavuma provided some home hope with a resolute innings in spite of the relentless pressure from the Australian attack, which had to do without Josh Hazlewood, who took a career-best 6-49 in the first test but was absent with an upset stomach.
No more rain is forecast for the rest of the test as Australia look to wrap up the three-match series. Extra time is to be added to all three sessions on Tuesday.