The centre-back was in the starting XI, partnering Frankie Kent in the middle of defence, but had to be replaced late on by Michael Steinwender.
McInnes revealed Halkett suffered a back spasm and he will likely be available for the next fixture against Livingston after the international break.
“Just his back. Aye. He’ll be fine on Monday, likely. No use to me on Monday! It’s just a spasm. He says [before the game], I can’t even get off the [treatment] bed here, never mind jump or run.
“When your back goes, it goes. Honestly, I couldn’t believe it, to be honest, but it is what it is. We’ve got to deal with these things.”
The disruption before the game added to the defensive injury issues with Harry Milne, Stephen Kingsley and Stuart Findlay all out injured.
McInnes and his coaching staff “had a discussion for a couple of minutes about how best to do it”.
“You could move Jamie McCart in and then maybe Altena at left-back, but we’ve worked on things this week where we just thought, just try and make one change,” he said.
“Michael getting in at centre back, obviously it’s not perfect from being at left-sided, but what it does do, it gives a wee bit of help to Frankie really, in terms of speed, running about him and covering the grounds and getting into their high eight at times and Westley, and in the main we dealt with it well.
“I thought Michael… I’m so pleased for him because he’s sometimes an easy target. I’m so pleased for him in his natural position. He turned up and did a great job, as they all did today.”