"It means a lot," said Stewart, whose previous Daytona Supercross win came in 2007. "I felt good all day. I was fastest in practice. Once I got in front, I was just trying to survive."
Rain showers throughout the day made for a muddy course. Due to the course conditions, AMA shortened the Supercross Main Event by four laps and the Lites Main Event by three laps.
Rounding out the podium were Millisaps in second and Honda's Kevin Windham in third.
Ryan Villopoto, the two-time defending Daytona Supercross champion and current AMA Supercross points leader, fell during the first corners of the race and salvaged a fifth-place finish.