Jowell turned down the BBC's original proposal last September on the grounds that BBC Three was not distinct enough from channels provided by the commercial sector. She has now ordered the BBC and Independent Television Commission to reconcile their wildly differing predictions on the size of the audience BBC Three would attract.
The order will effectively delay a decision on the channel by at least another month.
"I'm concerned about the impact on the ecology of broadcasting and particularly on commercial broadcasters,
she said.
The news prompted delight among commercial broadcasters. David Brook, director of strategy and development at Channel 4 said: "It is good news for licence-fee payers. BBC Three is promising to provide what already exists in the commercial marketplace - Channel 4 and E4."
An ITV spokesman said: "This is a sensible decision in the light of current market conditions. BBC Three is aimed at a market that is a key demographic for advertisers."
The Incorporated Society of British Advertisers also welcomed the decision.
Bob Wootton, director of media and advertising affairs, said: "BBC Three could cost commercial broadcasters up to £25m, further impoverishing them and ultimately diminishing their ability to attract the audiences we demand."
BBC chairman Gavyn Davies argued that each month of delay would postpone its £80m investment in new production.