Kubica had a best time of 1 minute, 19.157 seconds in 87 laps around the 2.751-mile Circuito de Jerez.
Hamilton was second in his McLaren in 1:19.331, while Schumacher's former teammate, Felipe Massa, was next in his Ferrari, clocking 1:19.333.
Schumacher had a best time of 1:19.885 from 67 laps, with Ferrari noting that the retired seven-time F1 world champion drove on experimental tires.
Last month, Schumacher was fastest in his two previous days of testing for Ferrari at Barcelona in his first time behind the wheel since his retirement in 2006.
The 38-year-old German returns to the track for the final day of testing on Friday.