Despite the stress fractures in his back keeping him out of cricket for most of 2016, Siddle still retained his contract with Cricket Australia for the 2016–17 season. He returned from injury in October to play for Victoria in three one-day games and a Sheffield Shield match and was selected to play another Test match against South Africa at the WACA. He had bowling figures of 1/36 and 2/62 in the two innings, as Australia lost the match by 177 runs. This looked like being his final Test match for Australia, as he was dropped from the side for the second Test with a back injury. During this summer, the Australian selectors worked on reshaping their bowling attack by focusing more on youth and outright pace, which left Siddle off of their radar moving forwards.