Djokovic failed to win a title from August onwards -- after claiming six in the first half of the campaign -- and relinquished top spot in the world rankings to Andy Murray.
He admitted to losing his motivation for a while and suffering from "private issues," while wrist and arm injuries also played a part in his slump.
The Serb ended his season with a crushing loss to Murray in the final of the ATP World Tour Finals, with the No. 1 spot on the line, despite the Scot playing a nearly four-hour match
the day before.
Rafter, though, is convinced the 29-year-old will rediscover his form and add to his tally of 12 majors next season.
"Djokovic will have a half-decent year again and win a couple slams," the Australian told CNN's Open Court.
Djokovic, according to two-time US Open winner Rafter, has the potential to reclaim the top ranking.
Winning two majors would certainly help his cause.
By contrast, Rafter isn't sure if Murray will be able to replicate his outstanding 2016.
"Will he be able to solidify it? I don't know," Rafter said of the Brit.
Like many, Rafter is also curious to see how Roger Federer fares on his return from injury.
Federer, who has won a men's record 17 majors, hasn't played since July. He decided to end his season after Wimbledon to recover from a knee injury that first surfaced in January.
The 35-year-old Swiss has dropped out of the top 10 for the first time since 2001. He was due to play in this month's Indian Premier Tennis League but due to financial constraints the exhibition event has not been able to enlist the top players it had targeted.
"If he's not winning a grand slam, is he struggling?" Rafter said of Federer, whose last major came back in 2012. "Because what is his goal? To be No. 5 in the world? I doubt it.
"I think he realistically thinks he can win another slam. Maybe he can. Whenever you are that great, you never write off a champion."