There was a stunned silence at the end of the game at Goldington Road as referee Ed Morrison consulted the rulebook and declared Bedford the winners by virtue of having scored more tries over the two legs.
Both sides got one as Rotherham won 19-11 last Thursday but Bedford scored three to Rotherham's two yesterday as the aggregate scores finished level at 38 - 38 as a dramatic end to the game saw Jake Niarchos for Rotherham and Bedford's Tony Yapp both missing kicks in the final minutes.
A distraught Rotherham captain Mike Schmid said: "We're all desperately disappointed. We worked so hard. But we can come bouncing back and try again next season.
"We'll try to keep the team together but if we have to buy new players to go one step further, then we'll have to. I thought Bedford played spirited rugby. They were hungry and maybe just about deserved the 27 - 19 victory today."
Rotherham's rise has surprised no-one at Bedford. "We have always had hard games against them," said the Bedford coach, Rudi Straeuli. "This was exactly the same. They played fantastically well and I admire them as a club and wish them well for the future.
"I thought the turning point in today's game was a try by our captain Alistair Murdoch, who ran one in from half-way just as we were coming under pressure."
.For Rotherham the rebuilding now starts for a third attempt to get into Division One. For Bedford there are off-the-field uncertainties. Thirteen players are out of contract.
Bedford: Tries Forster, Murdoch, O'Mahony; Conversions Yapp 3; Penalty Yapp; Drop Goal Yapp. Rotherham: Tries Lax, Scully; Penalties Niarchos 3.
Bedford : Stewart; Whetstone, Murdoch, Harris, O'Mahony; Yapp, Crabb; Olver, Richards, Boyd, Zaltzman, Murray, Cockle, Forster, Winters.
Rotherham : Umaga; Lax, Austin, Shepherd, Walker; Niarchos, Scully; Pinder, Garnett, Bunting, Webster, Kenworthy, Wade, Spence, Schmid.
Referee : E Morrison (RFU).