Honda's rookie set a 2m03.853s lap to outpace team-mate Dani Pedrosa by 0.123 seconds.
"Having a good pace early was important, because it allowed me to start to try things out," said Marquez.
"For the rest of the day we kept dropping our times and keeping to our strategy: testing things and confirming the results to eliminate any doubt.
"We did a great job today and the team is really helping me a lot. I am learning so much during these days - most of all with the electronics."
Jorge Lorenzo was top Yamaha rider in third, with team-mate Valentino Rossi behind LCR Honda's Stefan Bradl again in fifth.
Yamaha will not stay for the final day of running on Thursday, which team boss Massimo Meregalli said was always the plan.
"Today the results we got are quite promising and we are leaving Austin with a lot of useful data," he said.
"The test here was organised by Honda to cover three days but we knew from the beginning that two days would be enough for us.
"The target was to allow the riders to get used to the circuit and get as much data as possible for our Japanese engineers."
American CRT teams Attack and GPTech, both of which will make wildcard appearances this year, joined for day two but had troubled sessions.
1. Marc Marquez Honda 2m03.853s
2. Dani Pedrosa Honda 2m03.976s + 0.123s
3. Jorge Lorenzo Yamaha 2m04.351s + 0.498s
4. Stefan Bradl LCR Honda 2m04.640s + 0.787s
5. Valentino Rossi Yamaha 2m04.960s + 1.107s
6. Blake Young Attack APR-Kawasaki 2m13.641s + 9.788s
7. Michael Barnes GPTech BCL-Suzuki 2m13.993s + 10.140s
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- Dani Pedrosa