Jimmy Abdou's 74th-minute goal gave Millwall a 1-1 draw at Elland Road and a 2-1 aggregate win, and ended Simon Grayson's chances of leading United back into the Championship five months after becoming manager.
The former Leeds player had hoped to be planning a play-off final at Wembley this morning, but his thoughts were turning instead to a first full season as the Whites boss in English football's third tier.
Grayson said: "It's a bitter pill to swallow. The players were outstanding and they gave it a right go. I've got to be proud of what they've done and what they've achieved since I came here in December. I'm hugely disappointed, but the players have given their all for the club. It's hard to take because we wanted to be going to all the Championship teams next season. It's what the club deserves."