Bayern and Real both reported a net profit in the accounts used for the study, 2010/11 for the Spaniards and 2009/10 for their German rivals, according to Jose Maria Gay, a professor of accounting at the University of Barcelona.
The other two semi-finalists, holders Barcelona and Chelsea, by contrast, made losses in 2010/11 and 2009/10 respectively, the study showed.
Bayern, who will seek to protect a 2-1 lead when they play at Real on Wednesday, had the smallest debt among the four at 338 million euros, with Real's at 590 million.
Barca, needing to overturn a 1-0 deficit when they host Chelsea on Tuesday, had total debt of 578 million with Chelsea's by far the biggest at 792 million.
"Bayern typifies the German financial model characterised by reason, moderation and coherence," Gay wrote.
"Real Madrid, for their part, reflects more the Spanish model of a large conglomerate with substantial investments and a high level of debt."
Barca, chasing a third continental crown in four years, have "room for improvement both in terms of revenue and expenditure", according to Gay.
"The club has suffered in the past two seasons from a negative asset balance coupled with the losses they recorded at the end of each accounting period," he added.
"For its part, Roman Abramovich's Chelsea continues down the already familiar path of negative equity.
"The losses that build up season after season go hand in hand with the financing provided by the companies belonging to the club's owner.
"Its eye-catching equity deficit is nothing more than the result of returning negative results over a number of seasons."
Bayern also came out on top in a comparison of labour costs with revenues, the study showed.
The German side spent 201 million euros on labour against income of 350 million euros, or 57 percent of earnings, compared with Real's outlay of 309 million euros on revenues of 590 million, or 65 percent.
Barca's labour costs were the highest at 320 million euros compared with earnings of 450 million, or 71 percent, although both theirs and Real's includes a host of other sports teams within the clubs.
Chelsea's were 245 million euros on income of 229 million, or 107 percent.
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