Rafter had been among a number of observers to question Tomic's commitment before dropping the 20-year-old from February's tie against Taiwan.
Tomic subsequently stated he would be unavailable for the Davis Cup until September and it was unclear how the impasse would be bridged.
The world number 45 produced a woeful performance against Andy Murray at the Miami Masters on Saturday when he appeared listless and disinterested.
However, with Australia facing a tough clash against Uzbekistan on April 5-7, Rafter clearly feels he needs to field his strongest team with Tomic possessing huge potential.
Marinko Matosevic, Lleyton Hewitt and Matt Ebden make up the quartet that will contest the Asia/Oceania second-round tie.
Tomic is pleased to be back in the Davis Cup fold.
"I always want to play Davis Cup. I want to thank Pat for picking me. Wherever it is I'll always be happy to play for my country," Tomic told tennis.com.au.
"Lleyton has always told me what a huge thing Davis Cup is.
"We have a good chance to beat Uzbekistan. I'm back where I want to be, I'm looking forward to playing Davis Cup again and I'll give my best."
Rafter added: "We have a team which is very motivated to go into an extremely tough away tie and try and win our way to a World Group play-off.
"We are under no illusions as to the difficulty of the task ahead, but we want this badly."
A win over Uzbekistan would see Australia progress to a World Group play-off tie in September, and just one win away from returning to the elite 16-nation World Group for the first time since 2007.