Sagan appeared to force the British rider into the barriers with his elbow as the pair jostled for a good line in the final few hundred metres of the stage to Vittel.
'Cav's gone down!' - Cavendish suffers horrendous crash
And it was adjudged that the World Champion was indeed to blame for the incident.
'Something special' - Cavendish thankful for British support this year
'I just didn't know that Cavendish was behind me' - Sagan
An initial punishment saw Sagan docked 30 seconds and relegated to 115th in the field. But, following an appeal by Team Dimension Data, a subsequent ruling saw the Slovakian thrown off the Tour.
Eurosport's Brian Smith was strong when asked for his opinion on the incident, describing it as a "lack of respect".
'Sagan has made a huge mistake and it's not the first time' - Smith
And Smith predicted that the commissaires may take the decision that they ultimately did:
I don't want to see the World Champion thrown off the race. I don't think anybody would. I don't think Mark Cavendish would want that. It's a racing incident, but it was dangerous in the end. Everybody knows you don't flick that elbow out. As they were coming together Peter Sagan made a split (second) decision: 'This is mine. This is my wheel. I don't care what the consequences are'. He was fighting to get that stage win, and that's what they do, sprinters. And to flick that elbow on the end I think that's a little bit too much and that's classed as dangerous.
The news means that there will be a new winner of the Points Classification green jersey for the first time since 2011, with Sagan having won on each of the past five years.
Tour de Slovaquie
Einhorn soars past Sagan to win Stage 4 at Tour of Slovakia
Tour de Slovaquie
Halvorsen wins Stage 3 photo finish in Slovakia