All-rounder Ryan Harris will replace injured Australia pacer Peter Siddle for the Commonwealth Bank ODI series against South Africa starting January 16.

The 24-year-old Siddle has been ruled out of the opening two matches of the series after scans revealed early stages of mild stress on his left foot, Cricket Australia (CA) said on Tuesday.

"Peter Siddle has had previous pain in his left foot which became worse during the 3 Mobile Test Series against South Africa. After the series was completed, we investigated and scans revealed the early signs of mild stress on a bone in his left foot," Australia's team physio Alex Kountouris said. 

Kountouris, however, hoped that a brief rest will help Siddle recover and he could be available for the series against New Zealand next month. 

"As such, Peter needs a short period of rest before resuming bowling which we anticipate will be in a further two weeks. He is expected to take part in the Commonwealth Bank Series against New Zealand in February," he added. 

Meanwhile, right-hand batsman Michael Clarke will have an assessment on his injured right thumb tomorrow, while David Warner has been placed on standby for him and will travel with the team to Melbourne.