Portugal, who missed a spot kick given thanks to the video assistant referees 16 minutes into the match, were awarded a second penalty after 104 minutes when Miguel Layun handled the ball.
Leicester City's attempts to sign Adrien Silva from Sporting Lisbon were dealt a blow on Wednesday, with FIFA saying it had rejected an FA petition to grant the midfielder an international transfer certificate.
Portuguese club Sporting Lisbon are to complain to FIFA after three of their development squad players trained with Chelsea.
Any sliver of a doubt over whether Cristiano Ronaldo would lead Portugal into the Euro 2016 was erased on Tuesday when he was named in their 23-man squad for the finals.
The 31-year-old is still recovering from the knee injury which forced him to limp out of the Euro 2016 final against France in the first half, coach Fernando Santos said.
Talismanic Portugal captain Cristiano Ronaldo struggled against Croatia producing just one shot on goal, but coach Fernando Santos defended his "amazing" captain.
IMAGES from the FIFA World Cup Group B match played between Portugal and Iran in Saransk on Monday
Cristiano Ronaldo shows no signs of flagging as he approaches his mid-30s but there are plenty of other worries for a team with an ageing central defence and a number of players struggling for form.
Riyad Mahrez scored one and set up another as Leicester City strolled to a 3-0 win over Huddersfield Town in the Premier League on Monday.
Images from the football matches played across Europe on Tuesday.
Portugal coach Fernando Santos left Bernardo Silva, one of the country's brightest young players, out of his final 23-man Euro 2016 squad on Tuesday but included 18-year-old Renato Sanches.
Cristiano Ronaldo has been one of Portugal's biggest culprits, missing an easy chance late in the 1-1 draw with Iceland and firing a penalty against the post late in the Austria match.
Manchester United climbed back up to second in the table after second-half goals by Anthony Martial and Jesse Lingard earned a 2-0 victory at Everton -- their first win in five games in all competitions.
When France meet Portugal in Sunday's Euro 2016 final, the outcome is likely to depend on the performances of Cristiano Ronaldo and Antoine Griezmann -- the second time the two players have clashed with a European trophy at stake in six weeks. Portugal's Ronaldo steered Real Madrid to their Champions League triumph at the end of May after his French rival Griezmann missed a penalty for city rivals Atletico.
Portugal head into Sunday's Euro 2016 final after another disciplined performance, proving again in their 2-0 win over Wales that they perform like a well-rehearsed orchestra rather than a solo act. That has a huge amount to do with their 61-year-old conductor and coach Fernando Santos who took charge in September 2014, vowing to put "tactics first and technical ability second".
Having reached the Euro 2016 semi-finals without winning a game in 90 minutes it is probably time for Portugal fans to stop worrying about their misfiring forwards and instead give credit to the coach and defenders who have got the to the last four.
On a day of frenetic spending that took the Premier League total to a record far above one billion pounds ($1.29 billion), Antonio Conte's side also missed out on two of their other targets - Alex Oxlade-Chamberlain and Fernando Llorente.
Centre forward Eder, who scored the winning goal in the Euro 2016 final against France, was among 10 players from that squad omitted from Santos's list. Other unlucky players included midfielders Andre Gomes and Renato Sanches, forward Nani and defender Eliseu.
Manchester City paid the price for missed chances as they were held to a 1-1 draw at Burnley on Saturday with Johann Berg Gudmundsson's 82nd minute equaliser earning the hosts a share of the points.
Injuries have blighted Liverpool's start but Adam Lallana is back in full training after damaging his thigh pre-season and is expected to feature while another injury concern, Sadio Mane, also trained on Wednesday after tweaking a hamstring on international duty with Senegal.
News of all that's transpired on and off the football field
Aaron Ramsey scored a hat-trick on Saturday as Arsenal thrashed Everton 5-1 in the Premier League at the Emirates with a display of free-flowing football that the Gunners have sorely lacked away from home this season.
Real Madrid edged past Sporting Lisbon 2-1, while Juventus came from behind to secure a 3-1 win at Sevilla and Borussia Dortmund crushed Legia Warsaw 8-4 to set a record for the most goals scored in a Champions League match.
Ruthless Bayern Munich scored five goals in the first 35 minutes on the way to a 7-1 demolition of AS Roma on Tuesday which bore an uncanny resemblance to Germany's win over Brazil by the same score in the World Cup semi-final.