The way the rules interact is ambiguous, and depends on how one looks at the rules for potionmaking and universal potions.
"Yes" Interpretation: "Universal potions are potions"
Universal potions are, in their class feature, defined as "a potion." Brew Potion can be used to make all items in the subset of "potions," so it would work fine with universal potions. Thus, you can brew them of higher-level spells, although as noted in KRyan's answer, this creates a rules hole about their cost to create.
This interpretation is consistent with how the rules work in some other places, such as a "+1 flaming longsword" still being a "longsword," an "arcane spell" still being a "spell," and any other numerous pairings of adjective and noun not invalidating that noun's nouniness.
I personally lean towards this interpretation. It creates an unfortunate problem where you need to extrapolate the costs (thanks to the classes being from completely different books and settings), but it's the answer that fits best within the existing framework of 3.5 and the precedence of other abilities.
However, there are a couple ones on the opposite side of the spectrum that I think might be other likely conclusions:
"No" Interpretation: "Universal potions are potions, but..."
This interpretation hinges on the idea that universal potions, while they are potions (they're called out as such explicitly, after all), have their own special rules that override the normal rules for potions. Similar to rectangles and squares, all universal potions are potions, but not all potions are universal potions.
The question addressed by this interpretation is whether or not this exception to the normal potion rules:
To create a universal potion, you choose the maximum spell or infusion level it can hold (1st, 2nd, or 3rd). You then brew the universal potion, consulting the table below for the cost to create it.
Takes precedence over this one:
As Brew Potion (4th), except that the master alchemist can brew potions of 9th-level spells.
And it's a valid reading to say that it does override any and all other exceptions. D&D 3.5 is an exception-based ruleset, and juggling multiple rules that say opposite things is always an awkward scenario.
"No" Interpretation: "Universal potions are not actually potions"
This interpretation is similar to the above, but a bit more extreme. The idea behind it is that, regardless of the text describing it, a universal potion is as different from potion as an eternal wand is from a wand, or a runestaff is from a staff. Universal potions have their own special rules for creation listed in the ability, and they do not interact at all with normal potion rules. This interpretation would also lead to them not being able to be used with things like potion bracers, infusions that target potions, and the like. Of these three interpretations, this one causes the most rules breaks and has the least support, but it is still a possible answer here, because of the precedent set by the above three listed items. Personally, I do not think this is a very valid answer. It is a possible reading, but not a good one. Unlike with eternal wands, universal potions are explicitly called out as potions in their description.
So really, check with your DM
Most online D&D 3.5 optimization and builds assumes a permissive DM, because the game is broken in enough places that the DM's hand is needed for it to function. This is one of those cases, in my opinion. The rules interaction could be read in one of several ways, and a couple of those ways are fairly unfun. The most stringently-read way ("universal potions are potions; it says it right there in the ability") has a rules hole that results from it (like many combinations in 3.5), and is a bit stronger than the other ones.
I don't think that there's a true RAW answer either way here, however, so the best way to solve this is to build assuming the answer that enables the build, then to discuss the question with your group before using it.