Regulator Ofgem said the Competition and Markets Authority (CMA) probe should ensure "once and for all" that competition works effectively.
The investigation, is expected to take around 18 months. It will also study the Big Six's profits, as well as any barriers to entering the market.
Ofgem chief executive Dermot Nolan said: "There is near-unanimous support for a referral and the CMA investigation offers an important opportunity to clear the air. This will help rebuild consumer trust and confidence in the energy market as well as provide the certainty investors have called for." Ofgem said earlier this year that soaring household bills and intensifying public distrust highlighted the need for an investigation which will determine whether the Big Six companies were making excessive profits, after they quadrupled to more than £1 billion in three years.
British Gas owner Centrica has previously warned that the probe could create uncertainty and threaten the billions of pounds worth of investment needed to keep the lights on.
The CMA will begin its investigation immediately and is likely to publish final decisions by the end of 2015.
The Big Six, which dominate the energy market, are British Gas, SSE, E.ON, EDF, npower and Scottish Power.
Sam Laidlaw, chief executive of British Gas owner Centrica, said: "We want an energy market that is trusted by customers, and we believe an in-depth review by an independent authority can achieve this."