Instead, they won a draw without goals that reiterated the impasse against Sweden a year ago, which ended its hopes of reaching the World Cup in Russia.
"It is really satisfactory to reach the final stage of this competition," coach Fernando Santos said.
"But it was a very difficult game, above all the first half when I have to admit we have a lot of difficulties."
Portugal hosts Poland on Tuesday at Guimaraes in a match that has no meaning for either party.
But Santos insisted: "The final match against Poland will be important because it will be in front of our supporters who are always with us.
"We have to have a great match and win."
Santos beat Italy 1-0 in Lisbon and resisted the early pressure from the host, with Lorenzo Insigne and Ciro Immobile, both going in the first half.
Portugal threatened after the break, as William Carvalho was denied by Gianluigi Donnarumma and Joao Mario's substitution shot over the bar.
"I think we played an excellent match, but we did not manage to write what's an important detail," Mancini said.
"We dominated Portugal and then we had a drop in the tempo after 70 minutes, which is to be expected because we can not play in half for 90 minutes.
"Even though we are disappointed that we are not winning, I think we have everything and we will gradually attack the attack," Mancini added after Italy retained the file of never beating San Siro.
Chiellini's limit of 100
Italian captain Giorgio Chiellini celebrated Italy's 100th cap, exactly 14 years before the day he started off against Finland.
The badge forced a rescue from Rui Patricio after five minutes of firing from a distance, with the Portuguese goalkeeper cleaning up on Immobile's path.
But the Lazio team sent back the crossbar and Alessandro Florenzi sent an effort from an angle.
Former AC Milan defender Leonardo Bonucci whistled the crowd every time he touched the ball after moving back to Juventus this season, he headed for the side net in a free kick.
Federico Chiesa came close to 53 minutes after a shot from Cristiano Biraghi after a good job from Marco Verratti but the Portuguese defense was eliminated.
"I think we are on the right track, as we have been controlling it for 70 minutes with lots of play and chances, but we have to do more of our scoring possibilities," said defender Chiellini, Azzurri's big goal scorer with eight goals.
"We worked so hard and then we were exhausted for the last half hour, which led to clarity and meant that we were risky in the back.
"We have foundations, we have dominated the European champions, and the problem of gaps will not improve over time."
Italy plays a friend against the United States in Genk on Tuesday.