The 25-year-old striker, who had a spell on loan at Glanford Park two seasons ago, haunted his old club in an ill-tempered match which saw Leeds midfielder Jonny Howson sent off in the 80th minute for his second bookable offence.
Beckford, back from suspension, opened the scoring in the 32nd minute. Howson crossed from the right and keeper Joe Murphy failed to stop the striker's tame 10-yard shot going in off the near post.
Six minutes later Leeds were two-up. Robert Snodgrass took a short free-kick to Bradley Johnson, whose low shot deflected into the net off Grant McCann.
A misunderstanding between Rui Marques and goalkeeper Casper Ankergren allowed Gary Hooper to nip in for his first goal after 42 minutes and seven minutes after the break the Scunthorpe forward made an unchallenged run to equalise.
Beckford, though, fired an unstoppable 69th-minute shot past Murphy from close to the penalty spot for his 25th goal of the season before Howson saw red late on.