The Addicks chiefs was honoured at the LMA's annual event in Old Billingsgate in London after leading the east London club to the third-tier title with a club-record 101 points.
Charlton lost just five league games all season, with Powell also picking up three manager of the month accolades over the course of the campaign.
The 42-year-old becomes the first Addicks boss to win a manager of the year award since Alan Curbishley in 2000.
Former Charlton boss Alan Pardew won the Premier League award for his work at Newcastle, with Swindon manager Paolo Di Canio scooping the League Two award.
Brian McDermott, the Reading boss, took the Championship prize after leading the Royals to the title ahead of Southampton, led by former Iron manager Nigel Adkins.