Watson has been ruled out of the second Test against South Africa due to a calf complaint.
Speculation has been rife since the opening Brisbane Test that Clarke and Watson have not seen eye to eye.
The pair were said to have been in disagreement about the role Watson could play in Adelaide, particularly after the all-rounder suggested he would not bowl if selected in order to give his injured calf further time to recover.
Clarke quashed the rumours, saying there was no bad blood with Watson. “No, not at all. We have a great relationship firstly,” said Clarke.
“I know there’s been talk of that being a little bit different but Watto and I, our friendship and our professional relationship when it comes to captain and vice-captain, is as close as I can certainly ask for.
“We spoke daily even before we flew to Adelaide as a team and I was kept well and truly in the loop of where he was at, how he was travelling and what he was doing preparation-wise,” he added.
SA make two changes
Meanwhile, South Africa have selected Faf du Plessis to replace the injured JP Duminy for the second Test, while Imran Tahir has also been brought into the side. Du Plessis will make his Test debut today.
Photos: Shraddha Kapoor, Kim Sharma at 'Haseena Parkar' screening
Mumbai to Goa train: First look at the glass-top Vistadome coach
Shuttler Ashwini Ponnappa keeps it short and sexy on social media
Photos: Narendra Modi, others at Marshal Arjan Singh's funeral
Photos: Sussanne Khan and Nimrat Kaur spotted at a spa in Juhu