World champion Marquez made the fastest time of the day early on with his 1'59.115, despite making that time in his 13th of 79 laps, no other rider was faster.
Marquez was pleased afterwards, saying: "I'm happy because this morning we set a good lap, which is something important, but mostly I am pleased that we have completed all the work we had left pending from the first day. We're finished today with our homework done and I even had time to do a race simulation this afternoon, with a track temperature of 49°C.
"We have accomplished all the objectives we had set for this test, and now at the Qatar test our work will be more focused on the Grand Prix and fine tuning the setup of the bike. I do not think there are many more new things to try."
Pedrosa finished the day in 7th overall with a fastest time of 1'59.912, and he was pleased with how the bike performed.
He added: "Overall this second test went well. Today we were trying many different combinations for the electronics setup and we have managed to take a few positive steps forward.
"Obviously we still need to improve some things, but the good thing is that we are clearer about the setup we have to use and the areas in which we need to make further progress at the next test. It's been a pretty intense few days and now we have to try to adapt our findings in the best way we can, in order to continue progressing at the next test and the races."