Dr Thomas and Dr Sampath received the award in Chemical Sciences category and Dr Balaji in Mathematical Sciences.
The Rs 200,000 prize instituted by the Council of Scientific and Industrial Research almost four decades ago to recognise outstanding contribution to science and technology in the country, is given to scientists below 45 years.
Dr Singh also presented the first CSIR Award for science and technology innovation for rural development to the Chennai-based Central Drug Research Institute. Bangalore-based software company Tejas Networks India won the CSIR Diamond Jubilee Technology Award.
Both the awards carry Rs 10
In the Biological Sciences category, the award went to Dr Vinod Bhakuni of Central Drug Research Institute, Lucknow and Dr Rajesh Sudhir Gokhale of National Institute of Immunology, New Delhi.
Dr Virender Singh Sangwan of L V Prasad Eye Institute, Hyderabad won in the Medical Sciences category.
Dr Gufran-Ullah Beig of Pune-based Indian Institute of Tropical Meteorology and Dr Pulak Sengupta of Jadavpur University, Kolkata bagged the prize in the Earth, atmosphere, ocean and planetary sciences category.
In Engineering Sciences, Dr Ashish Lele of National Chemical Laboratory, Pune and Dr Sanjay Mittal of Indian Institute of Technology, Kanpur received the award.
Tata Institute of Fundamental Research, Mumbai picked up two awards -- Dr Atish Dabholkar in Physical Sciences and Dr Indranil Biswas in Mathematical Sciences.
Dr Sanjay Puri of the School of Physical Sciences, Jawaharlal Nehru University was awarded in the Physical Sciences category.