Yes, you can use "highest" to compare relative monetary amounts.
For example, OED definition IIIb:
Of a price, rate, amount, percentage, etc.: having a large numerical value. Also: (of a commodity) high-priced, expensive, costly; (of money) lent out at a high rate of interest; (of a currency) having a relatively high exchange rate.
But "highest" in the context of "scholarship" also means "the best," for example, this page from the University of Washington is titled "High Scholarship Recognition" and deals with dean's lists and Latin honors.
High Scholarship Recognition
Please refer to the General Catalog page on Dean's List for information about Quarterly Dean's List; Annual Dean's List; Baccalaureate Honors; Freshman, Sophomore, Junior, and President's Medals; and Honorary Societies.
In this context, I would read "highest scholarship" to mean the most prestigious scholarship offered, in terms of prerequisites. In other words, there's no scholarship for the top 1%. That said, it doesn't necessarily imply the money is the largest available (but it's likely); there could be a larger scholarship for really good football players, for instance.
If you want to emphasize how hard it was to get, "highest" is a good choice. If you only want to point out how much money it was, "biggest" or "largest" might be a slightly more accurate choice.