The "glancing" collision occurred on elevated track outside London Bridge station shortly before 5.30pm. Witnesses said both drivers braked sharply moments before the crash, which forced at least 10 of the trains' 16 carriages off the tracks.
Panic occurred as the estimated 200 passengers were plunged into darkness.
Seven people, including two elderly women, were winched from the wreckage.
Five passengers were known to have been treated for minor injuries. London Ambulance Service said it expected at least a dozen more were also slightly injured.
Railtrack and the two operating companies, Thameslink and Connex, last night began an investigation into the incident.
Witnesses said the Thameslink train, travelling between Brighton and Bedford, and the Connex South Eastern Dover Priory-to-London service were heading for London Bridge when one appeared to cut across the path of the other.Reuse content