Their bus plummeted down a slope in Wednesday's crash in the coastal town of Canico.
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An air force medical plane carrying the injured survivors of a bus crash that killed 29 German tourists in Madeira landed in Germany on Saturday.
The Portuguese driver and tour guide were among the 27 people who were injured when the bus veered off a steep road in the coastal town of Canico on Wednesday.
Eleven of the injured Germans have already been discharged from hospital. Another was transferred to Germany on Friday and one will stay in hospital in Funchal, Madeira's capital, a hospital spokesman said.
The driver and tour guide will also remain under observation in hospital, the spokesman added.
The company that owned the bus said it was cooperating with authorities investigating the crash. Many of the passengers were pensioners, German newspaper Bild reported.
Autopsies and post-mortem examinations have been concluded, Portugal's Justice Ministry said in a statement and authorities are waiting for data including fingerprints and dental records in order to confirm the victims' identities.
Although Madeira is a small island in the Atlantic ocean, it is visited by over a million tourists a year, which is more than four times the local population. There have long been concerns that its infrastructure, including its roads, cannot cope.