Melandri and Davies were fighting for third place in the early stages of the race when the GRT Yamaha rider went side-by-side with the Welshman at the long Turn 5 right-hander.
But the duo made contact and both ended up in the gravel, retiring from the race.
The incident between the two riders was investigated by race control, which decided to hit Melandri with a six-place grid penalty for the next race at Misano.
Davies criticised his opponent, saying his move was “ridiculous”.
Melandri, on the other hand, did not intend to apologise, saying Davies “was slow, and running on the outside line”.
A similar manoeuvre saw Jonathan Rea be penalised in Race 1 at Jerez after he divebombed Alex Lowes at the final corner of the race, sending the Yamaha rider into a crash.
Rea’s penalty was losing one position in the order, and he was also relegated to the back of the grid for the following race.