Scunthorpe manager Brian Laws faces a major rebuilding job during the summer after the club's second relegation in three seasons.
A 3-1 home win against play off-bound Swindon was not enough to save them heading back to League Two for the first time in nine years.
James Collins fired home from close range before a scrambled 87th-minute equaliser by Michael Collins and two minutes into stoppage time Mark Duffy fired them ahead from the penalty spot after James Alabi had been brought down by visiting keeper Wes Foderingham.
"We have got to rebuild again this summer and put the pride back into this club again," said Laws.
"Over the last few years Scunthorpe United have rightly been admired by many people in football for how much they have over-achieved by reaching Championship level.
"But the last three years have been difficult ones, with now two relegations.
"I know this club inside out and I'm prepared to do what we have to in order to get it back on track."
Swindon boss Kevin MacDonald said it did not matter who his side faced in the play-offs.
"All four teams in the play-offs are good ones and every game will be a difficult one," he said.
"Whether Brentford will be disappointed to have missed out on automatic promotion, I do not know. It's ourselves we have to concentrate on."