Blues boss Conte opted to deploy Brazil defender David Luiz in midfield in a bid to solidify his injury-hit team.
Luiz gave Chelsea the lead at Stamford Bridge on Wednesday, but although Eden Hazard doubled the hosts' advantage before half-time, Roma hit back impressively.
Aleksandar Kolarov's deflected strike reduced the deficit before Edin Dzeko netted with a brilliant volley and then a glancing header to put Roma ahead.
Conte admits Chelsea are in a 'big problem'
It took a late Hazard equaliser to stop Chelsea suffering a third successive defeat in all competitions, and Conte admitted his tactical switch had backfired.
"I didn't like the type of football we did for a lot of the game, but it's right to take the responsibility for this," said Conte. "I tried on one hand to protect my team, to become more solid and to move our central defender into midfield. On the other hand we lost totally our style of football. Sometimes you have to find the right solution to try to protect your team. Sometimes it's good, sometimes it's bad. Roma deserved this result."
Chelsea boss not Conte-nt with Premier League schedulers
Chelsea remains top of Group C, two points above Roma ahead of their second clash in Italy later this month.
But Conte is well aware Chelsea are in a difficult moment, with injuries and erratic performances threatening to derail their Premier League title defence and slow their progress in Europe.
Already without the injured N'Golo Kante, Danny Drinkwater and Victor Moses, the last thing Conte needed was more fitness problems in the Roma match.
But that's exactly what he got as Luiz suffered a calf injury that forced him off in the second half.
Tiemoue Bakayoko played on despite a groin problem, while Gary Cahill finished the game with his head heavily bandaged after a knock.
With Chelsea in the midst of a hectic period that includes matches against Watford, Everton, Bournemouth and Roma before the end of October, Conte was left to once again bemoan his growing injury list.
"You know very well our situation (with injuries). I have to praise my players because they showed a big commitment, otherwise we lose the game," said Conte. "After the first half the doctor told me Luiz had a pain in his calf, the same for Bakayoko in his groin. It was a good decision to protect Luiz. In this moment it is very important to protect the players. We must realise we had three important players out. This situation gives us problems, but I'm not looking for excuses."
Despite the frustration of seeing a memorable victory snatched away by Hazard, Roma manager Eusebio Di Francesco believes his side's fightback proves they are capable of slugging it out with Europe's top teams.
"We could easily have secured the three points but we should not forget we were 2-0 goals down," he said. "We had the right mentality. We have to grow from this performance. We made individual mistakes but the players who made those bounced back. They showed the right character. We are definitely on the right track."
Key to Roma's revival was a powerful display from former Manchester City striker Dzeko. "We know Edin scores lots of goals. It was a very good game by him," Di Francesco added. "When we go through difficult spells he can really overwhelm opponents and help the team."
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