The Spanish legend's career came to an end after his nation's defeat at the Davis Cup Finals last year but his early exit prevented the Serb from being able to attend his rival's swansong event - something that he regretted.
Djokovic told reporters at the Australian Open: "I don’t know the exact details as to how they envisioned the ceremony, but I know that the plan was to do it after the semis, if Spain were to go through.
"(Andy) Murray and I planned to be there, we couldn’t fit the quarter-finals in our schedule, but we were a sure thing for the semis.
"Unfortunately, it turned out the way it did, what are you going to do? More than that, I don’t really know.
"I saw the video [of the ceremony]. I don’t know if Rafa maybe didn’t want to make too much of a fuss about it in order not to bother other teams' matches … I don’t know, to be honest, but I feel bad that I wasn’t there."
However, Djokovic is able to look back fondly on the memories he shared with Nadal in the final year of his career.
The 24-time major winner said: "We were together on the court in Riyadh [at the Six Kings Slam]. That was the moment, a nice moment.
"I saw him play at Roland Garros, we played each other at the Olympics.
"The ceremony, if you want my opinion, wasn’t done properly.
"Maybe Rafa himself wasn’t sure whether he’ll play or not, if he can play some more, and then maybe it was too late to do something bigger. I don’t know, really."