The tall Morkel said better use of the rising ball, and denying Clarke scoring singles, were part of South Africa's planning for Australia's in-form leader ahead of Thursday's Test.
Morkel says the Proteas had to be smarter in their approach to Clarke after his unbeaten double-century in last week's drawn first Brisbane Test.
Clarke was named the man-of-the-match in Brisbane for his third double-century of the year, his unbeaten 259 which turned the match away from the Proteas over the closing two days after coming with his team wobbling at 40 for three on Sunday's third day.
The Australian skipper is the highest scorer in Tests this year with 1 041 runs and averaging 115.66.
"Any batsmen struggles a bit at first with the short ball so we will probably come up with game plans and start working on those sort of things," Morkel told reporters on Monday.
Plan to use short ball
"Definitely that is a plan to always use a short ball – you have got two short balls an over so why not use it.
"We just need to use it in a clever way and see how we go from there."
Morkel said the South Africans had to put Clarke under greater pressure in Adelaide.
"He played very, very well," Morkel said. "If we can create more pressure and try and stop him from rotating strike that will be key."
Morkel said the South Africans would also address their costly spate of no balls in the Brisbane Test, where Proteas bowlers over-stepped 23 times.
Morkel was denied Ed Cowan's wicket because of a no ball while Australian quicks Peter Siddle and James Pattinson also lost wickets due to no balls.
"It's a controllable," Morkel said.
No-balls also targetted
"It is something I personally have been working hard on ... the stats show we have been bowling quite a lot [of no balls] over the past few Test matches and Test series so it's definitely a thing that we are targeting at the moment."
Meanwhile, Australian vice-captain Shane Watson said he was hopeful of proving himself fit for the second Test, but he has ruled out any possibility he might bowl in the match.
All-rounder Watson, troubled by a calf injury, batted and did some light fielding at training on Monday and will need to intensify his workload before Thursday's start of play.
"So far so good. I jogged around the field and got a bat as well – got through fine," Watson said.
"At this point in time, the most important thing is to be able to run consistently without really hurting it so bowling at this point of time is out.
"For me, it's just getting out to run around and do the skills I need to do to be fit to play as a batsman to start with." – Sapa-AFP