The metric took into account not only those factors, but combinations of the three. For instance, companies received separate scores in "profitability and growth" and "profitability and value" categories.
Copart took in revenue of $1 billion in 2013 and currently sits at a market cap of about $4.5 billion. Despite getting dwarfed by other top American companies, Copart vaulted to the top on the strength of its value and profitability, Deloitte wrote.
Read MoreSigns of optimism among family-owned businesses
While Copart is not a household name, it has enjoyed "truly a stunning run in performance over time," Raynor said.
The company was trading slightly higher on Tuesday just below $36 per share.
Hershey and Panera Bread followed Copart on the list. Deloitte rated profitability as Hershey's strongest area, while Panera's growth was highly touted.
Here are the top 10 companies in Deloitte's "Exceptional 100":
3. Panera Bread
4. Monster Beverage
5. J.B. Hunt Transport Services
7. Steven Madden
Raynor stressed that Deloitte's measure did not seek to show the absolute definition of a good business. It tried to illustrate what "exceptional performance" can look like according too one system, but does not mark the ultimate measure of a quality business, he said.
Copart was not immediately available to comment on the ranking.
Read MoreEarnings guidance: Survey says many don't need it
Read Deloitte's full study here.