The Catterall wheelchair racer had to settle for seventh place in the T34 400m final at the London Stadium.
In the final event of the evening, the 18-year-old former AKS pupil was drawn in the outside lane but was quickly overtaken by Walid Ktila of Tunisia, who went on to retain his title in a championship record time of 50.56secs.
MohamedAlhammadi of the United Arab Emirates was second (50.94) and Finland’s Henri Manni third (54.66).
Catterall-based Towers’ time of 54.66 was more than two seconds outside his personal best and 0.3secs behind fifth-placed GB team-mate Ben Rowlings.
The race was valuable experience for Isaac, who knows his best event, the 800m, is yet to come on Thursday.
It is over two laps that Towers was crowned European champion in Italy last year and reached the Paralympics final in Rio.
The T34 category is for athletes with cerebral palsy.