The Giallorossi drew 0-0 at Stadio Carlo Castellani on Sunday, in a game most notable for a number of saves Skorupski pulled off.
Being held by one of the league's smaller sides was frustrating for the visitors, but Nainggolan argued that there was not much more Luciano Spalletti's side could have done to try and secure all three points.
"We had the chances today and we tried until the end," Nainggolan said. "Skorupski made some big saves and was the man of the match. The only positive is that we didn't concede.
"It's hard to take if a team like ours doesn't score after five or six chances. Football is like this, it's made of individual episodes. If you don't score, you won't win."
He added: "No-one would have had any complaints if we had scored three today. We tried hard, played well and created chances. The important thing is that we're creating chances. If we hadn't done that, we'd be talking about a much worse situation right now."
Nevertheless, the result leaves Roma four points adrift of Juventus in the league, on a weekend where the reigning champions overcame last year's runners-up, Napoli.
"Whether it's four points or two, it doesn't change anything," the Belgian added. "We've got matches against them coming up and there's a long way to go. Had we won today, it would be a completely different story.
"Instead we drew and we should learn from our mistakes and get back to winning ways."
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