Todd picked his moment to perfection to fire past Boro keeper Ian Dunbavin with the clock ticking down and sent the home supporters into raptures.
Buoyed by their excellent win on Saturday, which secured them the title, Stanley could have been forgiven for taking their foot of the peddle with the silverware already in the bag.
And that was the way it proved as the table toppers struggled to make their class show.
However, Todd's late goal was a deserved award for a battling display against opponents fighting against relegation at the other end of the table.
In fairness Scarborough were the better side in the first half and had some excellent chances.
Neil Redfearn shot wide after only two minutes and in the 13th minute Denny Ingram was unlucky with a powerful shot which flew wide of the post.
In the 17th minute Redfearn had another good chance, but his fierce drive was well saved by Accrington keeper Rob Elliot.
Stanley finally found their footing and with 25 minutes gone goalscorer Todd saw a shot saved by Dunbavin.
Two minutes later Romauld Boco missed the target from close range, while at the other end Ingram fired wide after a bright move from the visitors.
Redfearn, at the heart of the visitors' best action, again fired wide in the 41st minute and with a minute to go before the break, Tony Hackworth failed to test Elliot when in a good position.
Champions Stanley nearly took the lead on the stroke of half time, but Mark Boyd saw his shot fly over the crossbar.
The re-start saw Scarborough on the attack once again and Kevin Nicholson fired wide in the 48th minute.
At the other end, Danny Ventre missed the target, before Scarborough had two good chances to take advantage.
Redfearn was guilty of missing another clear cut chance and then Chris Hughes missed the target when he should have done better.
Substitute Andy Mangan fired wide for Stanley in the 58th minute, before Scarborough saw Nicholson have a shot saved by Elliot.
In the 66th minute, Robert Atkinson was unlucky with a powerful header which Elliot did well to deal with, before Scarborough's plight wasn't made any easier when Hughes was dismissed for serious foul play.
Down to ten men and facing the Conference champions, Scarborough struggled to pressure their opponents and had one more good chance. It fell to Redfearn who, once again, was not clinical enough when he needed to be.
Todd forced Dunbavin to produce a smart stop in the 76th minute, but Stanley's perseverance finally paid off in the dying seconds when Todd rose above Scarborough's defence to head home.