Cueto (4-0) missed several turns in the rotation while recovering from a strained lateral muscle but showed few signs of rust Sunday, yielding five hits without a walk.
The right-hander struck out three as the Reds took the rubber match of a three-game set.
Jay Bruce socked a solo homer and Donald Lutz provided a pinch-hit, two-run single to pace Cincinnati's offense.
Wily Peralta (4-8) was hung with the loss, surrendering five runs (four earned) on seven hits over 5 1/3 frames.
Carlos Gomez belted a bases-empty homer for Milwaukee.