The U's scored the opener 10 minutes before the break after Kevin Amankwaah was brought down in the Braintree box, when former Middlesbrough midfielder Nicky Bailey beat goalkeeper Sam Beasant for his third goal of the season.
Isaac equalised in kind just before the break as he fired home from the penalty spot following a foul by Louis John.
Beasant did well to tip Amankwaah's header over the bar after 50 minutes and put in a diving save to deny Chris Dickson, while - at the other end - Ross Stearn's attempt to find the top corner missed by inches.
The away side lost Ian Gayle to a red card with seven minutes remaining but Isaac completed his brace at the end when his 25-yard strike beat Ross Worner to clinch all three points.
Match report supplied by the Press Association.
Match ends, Sutton United 1, Braintree Town 2.
Second Half ends, Sutton United 1, Braintree Town 2.
Goal!  Sutton United 1, Braintree Town 2. Chez Isaac (Braintree Town).
Ian Gayle (Braintree Town) is shown the red card.
Craig Braham-Barrett (Braintree Town) is shown the yellow card.
Substitution, Braintree Town. Joe Maybanks replaces Sam Matthews.
Substitution, Sutton United. Ryan Burge replaces Craig Eastmond.
Substitution, Sutton United. Maxime Biamou replaces Gomis.
Substitution, Sutton United. Roarie Deacon replaces Bradley Hudson-Odoi.
Substitution, Braintree Town. Lee Barnard replaces Brandon Goodship.
Second Half begins Sutton United 1, Braintree Town 1.
First Half ends, Sutton United 1, Braintree Town 1.
Substitution, Braintree Town. Jon Ashton replaces Jake Goodman.
Goal!  Sutton United 1, Braintree Town 1. Chez Isaac (Braintree Town) converts the penalty with a.
Ross Worner (Sutton United) is shown the yellow card for a bad foul.
Goal!  Sutton United 1, Braintree Town 0. Nicky Bailey (Sutton United) converts the penalty with a.
Sam Corne (Braintree Town) is shown the yellow card for a bad foul.
Daniel Wishart (Sutton United) is shown the yellow card.
Ian Gayle (Braintree Town) is shown the yellow card.
First Half begins.
Lineups are announced and players are warming up.
Chez Isaac netted in each half as 10-man Braintree returned to winning ways with a much-needed victory over Sutton at Gander Green Lane.