Paul Merson's tenth minute penalty and Todorov's brace in the first half proved enough to give Pompey an unassailable lead at the top over rivals Leicester.
The victory clinched manager Harry Redknapp's fourth major championship in 16 years and the boss and his players received a standing ovation from the happy 19,420 crowd as they embarked on a lap of honour at the final whistle.
Portsmouth entered the game knowing that victory over the Merry Millers would be enough to win the title after Leicester could only manage a 1-1 draw with Norwich but Rotherham proved hard opponents and twice threatened to ruin the title party by cancelling out Portsmouth's advantage.
Pompey made the perfect start as they took the lead through Merson's 12th goal of the season as he gave keeper Ian Gray no chance from the penalty spot after Todorov had been fouled in the area by defender Guy Branston.
Branston made amends six minutes later as he took advantage of slack Portsmouth marking to sidefoot home from six yards after Portsmouth had failed to defend Shaun Barker's long throw from the right.
But the defender's joy turned to despair in the 22nd minute as he allowed Portsmouth to regain their advantage with an error on the right.
Vincent Pericard easily escaped from his marker to cross invitingly for Todorov to finish from close range to net his 22nd goal of the season.
Rotherham defender Chris Swailes cancelled out Portsmouth's advantage for a second time on the half-hour mark when he headed home unchallenged from a corner and it seemed Pompey might fluff their lines.
But Todorov was on hand in first-half stoppage time to produce a cool finish from Pericard's knockdown to settle the home side's nerves and his strike proved enough to send Portsmouth over the moon with joy.