The Australia captain retired hurt with a back injury during the afternoon session on day one in Adelaide, having compiled 60.
But, after receiving injections to ease his pain, Clarke accompanied Steven Smith to the crease first up on Wednesday before going on to collect his 28th Test hundred.
Clarke (128) and Smith (162 not out) put on 163 for the seventh wicket as Australia reached stumps on 517/7 on a day where only 31 overs were possible due to rain.
Clarke, who had initially battled a hamstring strain to figure in this match, crunched his fourth ball of the morning, delivered by Mohammed Shami, for four and went on a record seventh hundred at the Adelaide Oval.
The 33-year-old grimaced his way to three figures, which he brought up by clipping a single off his pads off Varun Aaron???s seam, before he was caught out late on by Cheteshwar Pujara.
Smith, meanwhile, was in sumptuous form as he posted his highest score in Test cricket, currently 24 more than his previous best of 138 not out against England at The Oval in 2013.
New South Wales players Clarke and Smith kept their composure during a number of rain delays to back up the good work carried out by first-day centurion David Warner (145).
Both batsmen raised their bats to the sky when reaching hundred as a tribute to fallen team-mate Phillip Hughes, who died after being struck by a bouncer in a Sheffield Shield match in late November.
Clarke holed out off the leg-spin of Karn Sharma in the closing stages of day two and after Mitchell Johnson came out to bat, the umpires took the players off for bad light.