Inter had feared expulsion from next season's Champions League given that this was a second offence but a UEFA disciplinary panel instead imposed a £132000 fine (300000 Swiss francs) and ordered to play six matches behind closed doors two of which are suspended for three years.
AC Milan's keeper Dida was struck and burned by a flare thrown during a barrage of missiles during the match on Tuesday night and his side have been awarded the match 3-0 meaning they play PSV Eindhoven in the semi-final.
UEFA communications director William Gaillard denied Inter had escaped lightly.
He told BBC Radio Five: 'There will be some people who think that it is lenient and other people who think that it is harsh.
'This is the highest fine in the history of UEFA and the loss of four home games will mean they lose out on revenue for around 8 million euros (£5.5million).
'You have to put it in the context of the game. There were no further injuries apart from a very slight one to the goalkeeper which we absolutely regret and it is a very hefty punishment compared to anything in the last five years.'
Inter were represented at the disciplinary hearing in Nyon Switzerland by their president and most illustrious former player Giacinto Facchetti who left UEFA headquarters looking grim-faced but he must have been a relieved man.
In 2001 Inter were ordered to play two European home matches away from the San Siro and fined £35000 (75000 Swiss francs) after similar crowd trouble at their UEFA Cup game with Spanish side Alaves and they have also have a serious problem with hooliganism from their 'ultras' the extremist fans attached to most Italian clubs.
Had they been expelled from next season's Champions League Inter would have lost around £10million in television money and bonuses and a further £8million in match-day takings.
Given that their punishment can be increased if they appeal - they have three days to do so - it seems very likely that Inter will accept the punishment.
Should there been any more crowd trouble at their European games the two-match suspended ban will be imposed immediately on top of any new disciplinary sanctions.
The decision not to expel Inter however means that any other club up for similar crowd violence will be able to argue they too should been given at least two chances before they are excluded from European competition.