Troncon is sidelined with a knee injury and flanker Andrea De Rossi will skipper the Azzurri for the first time in this competition.
"Paul is in great form," Kirwan said. "His decision making and his passing is very good.
"You cannot make a comparison with Troncon - they have different qualities."
Benetton Treviso stars Santiago Dellape and Denis Dallan have passed fitness tests and are in the side.
Kirwan has opted for Nicola Mazzucato's experience with Stade Francais player Mirco Bergamasco relegated to the bench although Andrea Masi will play at full-back, a position the younger Bergamasco brother has also filled in the past.
Bergamasco has been unable to fully recover from a thigh injury picked up in training.
There are four uncapped players in the 22-man squad, including Griffen.
Teams for Italy versus England, RBS 6 Nations Championship, Stadio Flaminio, Rome, Sunday, 3pm (GMT).
Italy: A Masi (Viadana); N Mazzucato (Calvisano), C Stoica (Montpellier), M Dallan (Treviso), D Dallan (Treviso); R Wakarua (Brescia), P Griffen (Calvisano); A Lo Cicero (Lazio), F Ongaro (Treviso), M Castrogiovanni (Calvisano), S Dellape (Treviso), M Bortolami (Padova), A De Rossi (Calvisano, capt); A Persico (Leeds), S Parisse (Treviso).
Replacements: S Perugini (Calvisano), C Festuccia (SKG Gran Parma), C Checchinato (Benetton Treviso), Silvio Orlando (Benetton Treviso), S Picone (Benetton Treviso), R De Marigny (Overmach Parma), M Bergamasco (Stade Francais).
England: I Balshaw (Bath); J Lewsey (Wasps), W Greenwood (Harlequins), J Robinson (Sale Sharks), B Cohen (Northampton); P Grayson (Northampton), A Gomarsall (Gloucester); T Woodman (Gloucester), S Thompson (Northampton), P Vickery (Gloucester), D Grewcock (Bath), B Kay (Leicester), J Worsley (Wasps), R Hill (Saracens), L Dallaglio (Wasps, capt).
Replacements: M Regan (Leeds), J Leonard (Harlequins), S Shaw (Wasps), C Jones (Sale Sharks), M Dawson (Northampton), O Barkley (Bath), H Paul (Gloucester).
Referee: Andy Turner (South Africa).