The burly 32-year-old finished with 19 goals in 26 games despite sitting out the last six weeks of the season with a knee injury which required surgery.
"It's something special, it's my first title," said Meier.
"I can only thank the team and our fans for helping me to win it.
"I was realistic about my chances of winning it after my operation and thought I'd missed my chance."
Bayern Munich pair Arjen Robben, who spent the last two months of the season on the sidelines, and last season's winner Robert Lewandowski finished joint second with 17 goals each despite playing 21 and 31 games respectively.
Lewandowski added to his tally when he converted a first-half penalty in Bayern's 2-0 win over Mainz on Saturday as Pep Guardiola's side were crowned German champions for the 25th time.
Aubameyang scored in Dortmund's 3-2 win at home over Werder Bremen as his side finished seventh on Jurgen Klopp's last home game as Borussia coach.