The defending World Champion was one of only two riders to register a lap time of under two minutes, with his lap of 1:59.844 giving him a 0.058s advantage over Jorge Lorenzo.
Conditions have not been ideal for testing, with intense heat making life difficult for the teams, while Marquez also had to contend with a brake problem on the opening day.
With this in mind the Honda rider declared himself pleased with Tuesday's efforts.
"I'm happy because today was a positive day. After what happened yesterday, we tried to make up for lost time and tried out quite a few things," he told the official World Superbike website.
"Tomorrow we have to continue testing things out, in order to continue developing and eliminating anything that is not going to be useful. Today we focused on electronics and tomorrow we will work more on the chassis.
"I'm happy with how things went today and with the pace that we have achieved. We'll see if tomorrow the rain holds off all day, because we need good weather."