Luis Enrique was jeered by the Stadio Olimpico fans after Roma crashed out of the Europa League in a 1-1 draw with Slovan Bratislava.
Coach Enrique ran into a lot of controversy after the first leg 1-0 defeat by fielding Francesco Totti and Marco Borriello only for the last 15 minutes. The captain was in the starting XI with Bojan Krkic and youngster Caprari at the Olimpico, but Borriello was in the stands after being put on the market.
The Giallorossi were forced into a substitution within seven minutes, as Cicinho went off with muscular problems.
Moments later, Perrotta broke the deadlock to level the tie on aggregate. The midfielder came sliding in at the back post to turn in a Totti corner kick.
Fabio Simplicio drilled just over and Bojan's curler was charged down by Cikos. Totti attempted to curl in directly from the corner flag, but hit the side-netting.
Jose Angel aimed a couple of long-range efforts, though Maarten Stekelenburg also had to be careful on a Guede' snapshot. In first half stoppages, Aleandro Rosi combined with Bojan only to fire the right-foot finish inches past the post.
After the break goalkeeper Putnocky flew to parry a Totti strike from the edge of the box, then scrambled across as Caprari's curler skimmed the upright. Youth team product Caprari also tested the shot-stopper, while Jose Angel flashed an effort inches past the crossbar.
Enrique substituted Totti with 15 minutes to go and the tie heading for extra time, earning jeers of protest from the Olimpico fans.
The whistles from the crowd grew deafening soon after, as Slovan scored a crucial away goal. Marco Cassetti's poor clearance from Guede' was straight into the path of Stepanovsky, who comfortably tapped in the rebound.
It meant Roma had to score two goals in the final eight minutes to reach the Europa League. Stefano Okaka, who replaced Totti, wasted a great opportunity by firing straight at the goalkeeper in a one-on-one set up by Bojan.
Roma will spend this season out of Europe after crashing out 2-1 on aggregate in the play-off.
Roma 1-1 Slovan Bratislava (1-2 on agg)
Scorers: Perrotta 11 (R), Stepanovsky 82 (S)
Roma: Stekelenburg; Cicinho (Rosi 7), Cassetti, Burdisso, José Angel; Viviani, Perrotta, Simplicio; Bojan, Totti (Okaka 74), Caprari (Verre 69)
Slovan Bratislava: Putnocky; Cikos, Dobrotka, Had, Pauschek; Bagayoko, Zofcak (Dosoudil 92), Grendel (Stepanovsky 66), Guede; Kladrubsky, Sebo (Lacny 88)
Ref: Ozkahya (Tur)