"Di Francesco has left the club with immediate effect," the club said in a statement, without making it clear whether he had resigned or been sacked.
"The club would like to thank Eusebio for his work during his time at AS Roma and wish him success in the future."
Italian media reported that Claudio Ranieri, fired by English Premier League side Fulham last week, was a possible replacement.
Ranieri was previously in charge of Roma for one-and-a-half seasons between 2009 and 2011, taking them to second place in 2009-10 after they had led the league table until the last few matches.
Roma lost 3-1 at Porto in the second leg of their round of 16 tie on Wednesday and were knocked out of the Champions League 4-3 on aggregate, the decisive goal coming from a penalty three minutes from the end of extra time.
Although Roma are fifth in Serie A, they have had a rollercoaster season with defeats by Udinese, Bologna and SPAL, all teams in the lower half of the table, and squandered two-goal leads against Cagliari and Chievo.
They were thumped 7-1 by Fiorentina in the Coppa Italia last month and on Saturday they suffered a painful 3-0 derby defeat by Lazio.
They have 44 points from 26 games, three behind Inter Milan who are in the lowest of the Champions League qualification slots.
Di Francesco, a player in the Roma team which won the Serie A title in 2001, was in his second season as coach of the club.
He led them to third place in Serie A last term and the Champions League semi-finals after a memorable win over Barcelona in which they overturned a three-goal first-leg deficit, and had hoped to build on that this season.
"Since returning to the club, Eusebio has always acted professionally and put the club's needs ahead of his own," said club president James Pallotta.
There was a lot of sympathy for Di Francesco after the club sold three key players -- goalkeeper Alisson and midfielders Radja Nainggolan and Kevin Strootman -- before the beginning of the season.
New arrivals Javier Pastore, Bryan Cristante and Steven Nzonzi struggled to make a significant impact while captain Daniele De Rossi has been troubled by injuries.
The brightest spot for Roma has been the emergence of 19-year-old midfielder Nicolo Zaniolo, signed from Inter Milan in the close season.
(Reporting by Brian Homewood, editing by Ed Osmond and Christian Radnedge)
