The Queenslander qualified fifth and finished fifth after 12 laps around Portimao, having led at the end of the standing lap.
“Happy-ish,” he said.
“We left a bit on the table and I struggled at the beginning to get the feeling into the tyre and with the conditions.
“I made a small mistake with a mis-shift which cost me the tow with the front group but then I maintained the pace.
“Fifth was our maximum today so we’ll have a look in the areas we can improve.
“I felt really good at the end of the Sprint so fingers crossed we can carry that into tomorrow.”
Aprilia Racing’s Maverick Viñales won the Sprint, with Gresini Racing’s Marc Marquez and Pramac Racing’s Jorge Martin completing the podium on their Ducatis.
Miller had made a customarily good launch to lead the field initially after lining up on the middle of the second row.
He held top spot for a lap before Francesco Bagnaia (Ducati Team) went past on the run to Turn 1, but the Italian threw away the lead with an off at that corner on Lap 9.
Viñales inherited the lead and held it thereafter, while Marquez squeezed past Martin with a bold, final-lap move at Turn 5.
By then, Bagnaia had settled back into fourth, with Miller fifth.
The latter’s KTM team-mate, Brad Binder, was a DNF after crashing on Lap 4 at Turn 13.