Iannone crashed in first practice for the San Marino Grand Prix at Misano last Friday morning, and fractured the T3 vertebra in his upper back.
After some initial confusion, the Italian was ruled out for the weekend on Saturday morning, leaving team-mate Andrea Dovizioso and test rider Michele Pirro to represent Ducati.
Medical staff at the circuit indicated he would face a recovery time of up to 25 days, but the Austrian GP winner has signalled his intent to be back for the Aragon race on September 23-25.
"Really unfortunate," he told motogp.com of missing the race.
"I hope to recover very soon and hope to be at 80-90% [fitness] at Aragon, because it's very important for me to close this season at the top.
"It's very important to completely relax in these next few days, and hope for the best."
Iannone, who is moving to Suzuki in 2017, said he himself was confused about how he was ruled out of the race, having being declared unfit initially on Friday before then being classed as fit to be reviewed on Saturday morning.
The primary calls were made by the circuit's doctor, rather than doctors at the Cesena hospital Iannone visited on Friday or by MotoGP's medical team.
"I wanted to try my best to ride," he added.
"All the medical people explained to me that it's dangerous in case of a crash.
"I understood [this], but not 100% because before I arrived in Cesena, the medical team decided and declared me not fit this weekend - before I arrived at the hospital...
"When I came back, they changed the decision and declared me fit to be reviewed.
"[On Saturday] morning when I arrived, they explained, 'I'm sure you're not this fit'."
Dovizioso and Pirro finished sixth and seventh in Sunday's race, with Dovizioso moving past Iannone and into sixth place in the championship.