Midfielder Yossi Benayoun and forwards Gael Kakuta and Salomon Kalou suffered problems in Chelsea's 4-3 loss.
Kakuta becomes Fulham's second January signing following the permanent capture of Steve Sidwell from Aston Villa.
Ancelotti's thoughts on Chelsea's first-half performance were reflected in his decision to introduce Jeffrey Bruma, Kakuta and Drogba.
The club appealed against their punishment, claiming that Kakuta did not have a valid contract with the French club.
Gael Kakuta missed the crucial spot kick as Rovers won the shoot-out 4-3.
Kakuta went off at half-time after a tackle by Ryan Taylor, while Kalou himself was replaced in the 56th minute.
Ancelotti selected a young side and the match finished 3-3 after extra-time before 18-year-old Gael Kakuta missed his spot kick in the quarter-final tie.
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Both Kakuta and Chelsea were given bans that were subsequently overturned.
Football's governing body handed out a ban until 2011 after they found the Blues guilty of inducing Gael Kakuta to break his contract with Lens in 2007.
The 18-year-old Kakuta, who Chelsea controversially signed from Lens, struck the ball straight at Paul Robinson, who had earlier sensationally tipped Michael Ballack's spot kick on to the post.
Chelsea were found guilty by Fifa of inducing Gael Kakuta to break his contract with Lens in 2007 but the club have vowed to "mount the strongest appeal possible".
Chelsea trailed 1-0 at the break after a disappointing first-half performance, prompting Ancelotti to make a triple substitution at the restart with Kakuta, Jeffrey Bruma and Didier Drogba coming on.
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Kakuta has played for France at every level from Under-16 to Under-20 and in December 2009, aged 18, became the youngest ever player to represent Chelsea in the Champions League.
Kakuta's four-month FIFA-imposed suspension has also been lifted temporarily.
There was a lengthy interruption following a nasty collision between Kakuta and Steven N'Zonzi but it did not holt Chelsea's momentum and Kalou should have added a third with a free header.
It meant an opportunity for 18-year-old Gael Kakuta, at the centre of the transfer ban briefly imposed on Chelsea earlier this season after his move from Lens, while Joe Cole also started.
In addition, Chelsea were recently found guilty by Fifa of inducing Gael Kakuta to break his contract with Lens in 2007 when he was 16 which has opened up the debate on the tapping up of young talent.
In recent seasons, Chelsea have reduced the lavish spending that characterised the early years of Abramovich's reign, an approach that has seen greater first-team opportunities for some of their academy players, including forward Gael Kakuta, defender Jeffrey Bruma and midfielder Josh McEachran.
Chelsea even had the luxury of bringing on youngsters Gael Kakuta and Joshua McEachran as they comfortably closed out the game and deliver an early sign of their determination to end their Champions League jinx and win the competition for the first time.
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