I found the context of the above phrase in
Journal of the Chemical Society. Transactions. Vol. LXXI Part I, 1897. p. 727.
After referring to the fact that he had framed the diploma and hung it
up in his study, he says:
"To-day, the sight of this parchment is odious to me, and I feel
offended at seeing my name, with the qualification of virum
clarissimum which you have bestowed upon it, placed under the
patronage of a name doomed henceforward to execration by my country,
that of Rex Guilelmus."
In context, "Rex Guilelmus" refers to Emperor Wilhelm II of Germany. Diplomas of that time often used Latin. What Pasteur means is, he is offended that the diploma is signed by Wilhelm, or that it states his endorsement of the university (of Bonn), implying that he (Pasteur) is approved of by ("under the patronage of") Wilhelm, whose country has attacked France, and Wilhelm is therefore hated by the French people.