The 23-year-old, who has been capped 11 times by his country, has been ruled out of the final World Cup Group A qualifier due to a groin injury.
The setback is a major blow to Rhodes, who had been tipped to lead Gordon Strachan's strikeforce in the absence of Sunderland's Steven Fletcher and Shaun Maloney of Wigan.
Scotland have no chance of making next year's finals in Brazil but will be hoping to complete the double over Croatia having beaten them in Zagreb in June.
Strachan, who other options up front in the shape of Steven Naismith, Ross McCormack, George Boyd and Leigh Griffiths, has decided against drafting in a replacement for Rhodes.
Scotland assistant boss Mark McGhee said: "Jordan is a real blow. The manager feels a little bit frustrated that he's not been able to give Jordan a real opportunity.
"Jordan might have got that chance this time around and now he's out. That's a shame, we would have liked Jordan here but these things happen."
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