Fiorentina said the punishment was "profoundly unjust" in a statement on its Web site.
Liverpool face Lyon, Fiorentina and Debrecen while Chelsea play Porto, Atletico Madrid and APOEL Nicosia.
Meanwhile, Fiorentina booked their place in the last 16 with a narrow victory over Lyon in Florence.
In Italy, top clubs such as Fiorentina and Lazio have had trouble paying their players this year.
Sunday's victory gave Milan a five-point gap over fourth-placed Fiorentina, who lost 2-0 at home to Palermo.
Fiorentina showed a quality in terms of possession of the ball that we struggled to match at times.
"Many people were delighted we fell to Fiorentina but we've got back up, " Allegri told the match broadcaster.
Bari, meanwhile, moved up into fifth place on goal difference above a group of five teams including Fiorentina.
Milan need a new forward after selling Alberto Gilardino to Fiorentina, while Ronaldo has a serious knee injury.
In Italy, Serie A leaders Juventus dropped their first points of the season in a goalless draw at Fiorentina.
This time last season, Fiorentina was 16th, two spots above the relegation zone.
WSJ: Mortella's Approach Paying Off for Italian Soccer's Fiorentina
Fiorentina striker Adrian Mutu had earlier cancelled out Paulo Barreto's 25th minute opener.
Smith's side now face Serie A club Fiorentina, who followed up their win over Everton with victory over PSV.
Polish international goalkeeper Boruc and Scotland defender McManus are close to tying up moves to Fiorentina and Middlesbrough respectively.
The club confirmed that the Liverpool and Fiorentina matches were being investigated, but refused to comment further on the accusations.
Lazio president Claudio Lotito, Fiorentina honorary president Diego Della Valle and Reggina president Pasquale Foti are also among the accused.
The results mean Fiorentina qualify with 12 points, while Lyon are on 10 and can still finish as group leaders.
Remarkably, this Fiorentina side is packed with players who hit road bumps, whether through injury or poor performance, in their careers.
WSJ: Mortella's Approach Paying Off for Italian Soccer's Fiorentina
Milan's 13th win of the season moves it up to fourth in the league, leapfrogging rivals Inter, which plays Fiorentina Saturday.
Fiorentina stayed in contention by beating Palermo 1-0 with a first-half goal from veteran striker Luca Toni that relegated the visiting team.
As a result, Fiorentina has dominated most games, both in terms of chances and possession, though sometimes it comes at a price.
WSJ: Mortella's Approach Paying Off for Italian Soccer's Fiorentina
Udinese's 1-0 win over Cagliari sees them move up to fifth place, four points behind Fiorentina, who travel to Sampdoria on Sunday.
With his contract due to expire this summer, Kroldrup extended his stay at Fiorentina by agreeing a new two-year deal in May.
Inter Milan defender Maicon floated a 35-yard free-kick into the box and Fiorentina midfielder Melo out-jumped the American defense to head home.
Lazio are next on 36, followed by Inter 35 and Fiorentina 35.
In Italy, Roma missed the chance to draw level on points with fifth-placed Fiorentina in Serie A after they lost to Chievo Verona.
Montella and Fiorentina have earned plenty of plaudits this season, precisely because so much of what they've done has been both counterintuitive and effective.
WSJ: Mortella's Approach Paying Off for Italian Soccer's Fiorentina
Pazzini has been struggling with injury since the March 8 win over Genoa, but came off the bench late in the game against Fiorentina.
But, should Rangers beat Fiorentina to reach the Uefa Cup final, St Mirren will have to host the Glasgow outfit on Tuesday 20 May.
In other Serie A action, Fiorentina, who beat Liverpool for a famous Champions League victory on Tuesday, were held scoreless at home by Lazio.
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