Your intuition is right. The "set of molecules making up Caesar's last breath" is never completely well defined, but it has some approximate validity shortly after Caesar's death. In the long term, after thorough mixing, it's completely meaningless. This is true even in a toy model where you treat the atmosphere as an ideal gas (which I'll do in the rest of this answer).
In a quantum world it is not the case that "any particular molecule I'm breathing either was, or was not, in Caesar's dying breath", as one previous answer claimed. Particle indistinguishability is not a mere practical limitation on our ability to track particles or tell them apart. It's more fundamental. This seems to be a common misconception; two of the three earlier answers seem to suffer from it, as does the most upvoted comment on the question itself. The third earlier answer, which has a lot more upvotes, isn't incorrect but doesn't seem to actually answer the question.
It's probably easiest to understand this problem in the Lagrangian sum-over-histories picture. This isn't usually taught in introductory QM courses, but it is taught in Feynman's popularization of quantum electrodynamics which is well worth reading.
In the sum-over-histories picture you choose quasiclassical initial and final conditions – which in this case can be a bunch of molecules with precise positions and orientations in space – and you calculate the quantum amplitude of a transition from that initial to that final state, over that span of time, as the sum of contributions from all quasiclassical paths between those states. (In state-vector terms this amplitude is $\langle ψ_f|e^{iHt}|ψ_i\rangle$, where I'm taking $ψ_i$ and $ψ_f$ to be position basis states.)
The set of valid paths/histories includes paths that permute the sets of indistinguishable particles in all possible ways.* If the elapsed time between the initial and final states is small enough, and there's a speed-of-light limitation, some permutations are actually impossible, but that doesn't help us much in this problem given the small size of Earth's atmosphere in light-millennia. If the elapsed time is longer but still fairly short, all permutations are possible but the overall amplitude is dominated by paths in which the molecules don't move very far. It's therefore reasonable to say that, shortly after Caesar's death, the molecules from his breath are still, for the most part, nearby. This is not true in any absolute sense. It's not even true in a "statistically likely" sense, as all paths actually contribute to the transition and so all of them "happen". But it's about as true as any other statement you can make about a quantum world.
If the elapsed time is long enough that the atmosphere is thoroughly mixed, then all permutations of the whole atmosphere contribute essentially equally. The molecules are not permuted in any particular, random way. It's more like every molecule in the final state is a combination of every molecule in the initial state. There is no true path from start to finish, no merely-in-practice-unmeasurable correct permutation. This is true of any particular final state, at these long time scales.
* The set of valid paths does not include paths that exchange particles that merely have the same measurable properties (mass, charge, spin) but are not indistinguishable in the precise technical sense used in quantum mechanics.
For example, in a variant of quantum electrodynamics where there are many copies of the electron field (like the fermion generations of the Standard Model, except the masses are also the same, and there are no W bosons to complicate things), if you are given a bunch of electron-like particles, you can experimentally divide them into groups such that all of the particles within each group have Fermi-Dirac statistics, while particles from different groups have classical statistics. The fact that you can't say "which group is which", because they all have the same mass, charge and spin, is not what is meant by particle indistinguishability. The fact that the particles within each group have nonclassical statistics is what's meant by particle indistinguishability.
I'm mentioning this because I think it may be related to the misconception about Caesar's last breath. If there was just one electron in each group, and you let them interact unsupervised for a while and then tried to figure out which one had come from which group, it would probably be impossible in practice, but it is possible in principle, by the rules of quantum mechanics. If you took a bunch of electrons from the same group and let them interact for a while, it's impossible in practice and in principle to say which one was which. The latter case is the one that's relevant in the real world.