Resuming on 214-5, centuries from AB de Villiers and JP Duminy took South Africa to 423 all out.
In the reply, the tourists were reduced to 81-4 by Wayne Parnell and Vernon Philander before David Warner’s unbeaten 65 led them to 4-112 at the close, still 311 runs in arrears.
Lehmann was especially disappointed with his top order, with Chris Rogers, Alex Doolan, Shaun Marsh and captain Michael Clarke making just 32 runs between them.
“We’d love more first-innings runs,” he said.
“That’s what we need to do to get better as a cricket side.
“That’s probably the issue we’ve had in Test matches and got out of trouble with someone like Brad Haddin in a couple and obviously Shaun Marsh and Steven Smith in the last Test match.
“We’ve got to get better from our top order, we know that.
“It could have been worse if they took a couple of chances. They bowled very well, give them some credit there.
“I think the wicket is still very good and we probably helped with a couple of dismissals. We’ve got to be better in those tough situations.”