The American defied Friday's windier conditions to post a seven-under 66 for a total of 16-under 130.
Morikawa was the only player in the field to remain bogey-free through 36 holes.
The 25-year-old lies two shots clear of former Masters Champion Scheffler and 86th-ranked Spaun, who had rounds of 66 and 68 respectively.
Jon Rahm, who shared the lead overnight, dropped down the leaderboard to a share of sixth on 11-under 135 after a 71.
Three-time major winner Jordan Spieth was alone in fourth after a 66 that included two eagles.
Morikawa finished last year winless but fought his way into a share of the lead on the first day with six straight birdies before pushing ahead of the pack in the second round.
"Pretty solid, made some good putts. Obviously, it played a lot harder with kind of the wind, and just the fairways rolling pretty fast, you end up in a lot of spots where you're just going to end up in the rough," he said.
Morikawa has family connections to Hawaii and said he felt the local support.
"It's great. It definitely feels like home. Even though I never lived here. My Dad used to come all the time as a kid and grandparents are from here and great grandparents are from here and there's a long lineage throughout the Hawaii islands for us.
"It's nice to kind of feel that family, that ohana spirit around and just have people rooting you on," he added.
After playing his first 14 holes in three under par, Scheffler stormed home with four straight birdies from the 15th to rocket up the leaderboard.
"I hit some good shots toward the end, made a few nice putts, too," said Scheffler, who can return to the top of the world rankings if he wins this weekend.
"I've got to show up here and try to play good golf, and thinking about world rankings and stuff like that is not going to help me make good shots."