They quickly doubled their advantage four minutes later when Rory McArdle put a header past goalkeeper Lee Nicholls. The final result was then put beyond doubt when Nahki Wells volleyed in from close range.
Speaking to Sky Sports after the full-time whistle, Bradford manager Phil Parkinson said: "We've made a big step because getting out of this division is really difficult.
"We've got to look at it as the start of the journey because the potential at this club is huge."
Bradford's victory came 83 days after they lost the final of the Capital One Cup 5-0 to Swansea at the same venue.
A crowd of over 47,000 whilst not the highest for a League 2 Play-off final looks set to beat Sunday's gate for the League 1 final between Brentford and Yeovil. Whilst Brentford are expected to bring well well over 20,000 the Yeovil following may be much smaller.
Financially, Bradford will be in a strong position for next season, with two Wembley finals and the TV and commercial revenue from their Carling Cup run to boost the coffers.
On their second trip to the national stadium in three months, the Bantams ran out comfortable winners after three goals in the first 30 minutes.