The girl and boy, pupils at the £30,000-a-year Bedales school, were kicked out for 'sexual misconduct'.
A third pupil was expelled on suspicion of stealing whisky from a local supermarket.
The Daily Telegraph reported that the sex and drink scandal has centred around an end-of-term party held on June 29 on the grounds of the mixed boarding school in Petersfield, Hampshire.
The paper added that an anonymous teacher was reported to have written to parents, warning that the school was in crisis, saying: “As parents you need to ask 'who has lost their job' over the scandal that occurred when 13-year-old children (it could be your child) took drugs, drunk and had sex on the school premises and in school time.
“The total lack of care is shocking and you should be asking questions about the safety of your children and why certain members of staff are constantly protected.”
Headmaster Keith Budge wrote an official letter to parents of year nine students saying:
“On the penultimate Wednesday of term, four Block Three students were involved in a series of disciplinary incidents, starting with one of them stealing a bottle of whisky from Waitrose and ending up on their return from Petersfield in the sand quarry.
“Following a formal investigation of these incidents and further questioning at the resulting disciplinary hearings, I asked three of these students – two boys and a girl – to leave the school. One boy went for theft, the other two for sexual misconduct.
“This recent incident has highlighted misbehaviour of a small group of students, especially with regard to sexual behaviour.”
A spokesman for Hampshire Police said the force had 'consulted with the relevant authorities'.