The Shakedown test comes barely weeks after Gardner fractured his right wrist in a motocross incident, triggering surgery.
“Today has been a really positive day,” said the Sydney native.
“I am starting to feel better on the bike because we made some good changes.
“Although overall I can manage, I am still trying to deal with my wrist as it became a bit more painful as the day went by.
“Anyway, these days are for testing many things, it is all going smooth at the moment, I am enjoying the process, and I can't wait for tomorrow.”
Team-mate and fellow rookie Raul Fernandez was quickest with a 2:00.898s on Day 1 and fourth with a 2:00.819s on Day 2, during which he had a minor crash.
The Spaniard remarked, “The second day has been very positive for me as I continued my adaptation process to the MotoGP class.
“We worked very well and did many laps to try to understand different things.
“I think that the right approach is to focus on myself and get a lot of laps in without changing the bike too much.
“This is how I will adapt the most efficiently to the category, so we will continue in the same direction tomorrow.”
Maverick Viñales is the new pace-setter at Sepang, where he is eligible to ride by virtue of Aprilia's status as a concession manufacturer.
The Shakedown test concludes today.