Jonas was the third Power player to be suspended by the Match Review Panel in as many weeks for a bump on St Kilda's Dylan Roberton last weekend.
Roberton was concussed in the incident.
Hinkley admitted occasional suspensions were inevitable given the aggression he wanted from his side.
"Everyone knows the rules and you know the risk involved with the bump," Hinkley said.
"As a coach you've got to be able to say 'Well, he's playing an aggressive style of football that you want him to play' - at times if you do go a little bit close to the edge, it's (suspension) probably going to happen.
"It was a collision that was almost unavoidable to a point, when you're playing instinctive footy the ball's coming towards you, it's rolling through and you can see a player coming – I don't think you can stop that.
"We don't want to have people suspended, make no bones … but it's a contact game and there's going to be occasions where you can't control some of it.
"You've got to promote your players play hard footy."
Jonas has proved a revelation in defence this season and will be sorely missed against a Brisbane Lions outfit that could see the return of star forward Jonathan Brown on Sunday.
But Hinkley said there were two players who could step into the vacant key defender role.
"Paul Stewart certainly played a bit of tall back for us last week which 'Stewy' at 191cm gives us a chance – he's actually taller than Tommy Jonas," he said.
"We've also got (Jack) Hombsch that's in really good form, so we'll consider all of those options.
"His two games back in the SANFL he's played really strong footy, I watched him play two weeks ago.
"He's a young key defender that we think has a really bright future."
Hinkley was wary of the resurgent Lions, who are stalking Port's top-eight spot.
The Lions have won four of their last five games including come-from-behind victories against Geelong and North Melbourne.
Hinkley said he knew first-hand the benefit of confidence within a young group.
"They're a young side that are starting to get some belief and that's an amazing thing in football – we know that," he said.
"They've had a good five weeks of footy – won four and lost one – and once you get that going you start to believe in what you're doing.
"We've seen them in the NAB Cup, we've seen that side play really good footy; obviously they've got themselves some confidence."
Harry Thring for AFL Media. Follow him on Twitter: @AFL_Harry.
