Scott Boland was centimetres away from the second hat-trick of his Test in career in South Africa overnight, with the Gulidjan seamer continuing his knack of taking clusters of wickets on recall into the Australian XI.

With just 12.2 overs bowled on day one as rain took its toll in Gqeberha (formerly Port Elizabeth), Boland immediately validated the selectors' call to opt for a four-pronged pace attack in response to the especially green deck.

Rain delayed the start of play, and Boland returned from a second break with a maiden before landing back-to-back blows on the Proteas' top order.

The home side will resume play at 2-20 on Monday evening, Australian time.

Opening bat Aiden Markram was South Africa's best in the first Test and Durban, but couldn't resist an attempt to drive Boland mid-way through his second over.

Boland nipped the ball back down the line to flatten Markram's middle stump, before finding movement in the other direction the very next delivery.

David Bedingham went searching wide outside off stump before edging through to Alex Carey, leaving captain Temba Bavuma to face a hat-trick ball with his side at 2-12.

The Proteas skipper survived the hat-trick ball by getting bat involved when Boland found his front pad in the double-wicket maiden.

Boland's first Test hat-trick came against the West Indies in Jamaica last year.

After missing out for the first Test, Nathan Lyon was seen appearing to congratulate Boland with a handshake before the toss to signal his recall.

Rain washed out the afternoon with just 74 balls bowled on the opening day.

There is more rain forecast through the coming days.

It could make levelling the series a tough prospect for the home side after Matt Renshaw led Australia to a 214-run win last week.

Boland has figures of 2-5 after the small amount of play in the 20th Test of his career.

He featured in all five matches of last summer's home Ashes against England.