Armitstead, Trott and King were the leading three going into the final 14km lap of eight, but the Olympic road race silver medallist from London 2012 was not to be denied again.
Having had to settle for second place behind Sharon Laws last year, Armitstead, riding for Dolmans-Boels, attacked at the back of the course to build a 10-second lead in Glasgow.
Armitstead was all alone heading into the park for the final time, well ahead of Trott and King, and rode home for her second senior career Women's National Road Race Championship title.
And, while Armitstead was an assured winner, the battle for second went down to the wire between Olympic team pursuit champions from London 2012 Trott and King.
Trott, who also claimed omnium gold on the track at London 2012, edged out team-mate King in a sprint finish while another Wiggle Honda rider Jo Rowsell came home fourth.