Despite being smaller, they are packed with more vitamin C and compounds that may combat chronic diseases, the findings show.
The reason for the difference is down to the organic plants' tough upbringing, it is claimed. While conventional tomatoes are treated with pesticides and artificial fertilisers, organic farming forces the fruits to fend for themselves.
The stress they suffer as a result promotes greater concentrations of health-giving chemicals, according to the scientists.
Writing in the online journal Public Library of Science ONE, they argue that making life less easy for commercially grown fruits and vegetables can improve quality.
Opinions are divided over whether organic farm products really are healthier and worth the extra money.
A US review of research studies published last year found that while organic products may taste better, there is no evidence their nutritional value is higher.
The Soil Association, which criticised the review, insists organic farming is better for the environment and for health.
For the new study, scientists compared tomatoes grown on conventional and organic farms in Brazil.
The farms were located within one mile of each other and shared similar natural environments.
Fruits from 30 plants in each farming system were sampled and analysed.
Tomatoes grown on organic farms were 40% smaller than those produced conventionally.
However, their concentrations of vitamin C were up to 57% higher, and ripe fruits contained well over twice the quantity of phenolic compounds.
Plant phenols, such as flavonoids, help the body fight oxidative stress, a form of chemical damage linked to chronic conditions such as heart disease and cancer.