Group A wrapped up with South American powerhouse Uruguay moving to 9 points from their three matches, with Russia finishing second with six points.
Spain and Portugal progressed to the knockout stage from Group B, despite gutsy performances from their opponents Morocco and Iran.
It comes as the Socceroos look ahead to their clash with Peru on Wednesday.
Morroco 2 - 2 Spain
Spain snatched a 2-2 draw against Morocco to qualify for the World Cup last 16 and take top spot in Group B ahead of Portugal on goals scored.
Morocco striker Khalid Boutaib gave the north African side a shock early lead but Isco levelled, blasting high into the net after a layoff from Andres Iniesta.
Morocco, already eliminated, struck again in the 81st minute when substitute Youssef En-Nesyri crashed in a header which looked set to inflict a first defeat on Spain since Euro 2016.
But substitute Iago Aspas levelled in stoppage-time after consultation from the video assistant referee (VAR), putting Spain top ahead of Portugal.
Spain will take on hosts Russia in the knockout stage.
Portugal 1 -1 Iran
Portugal qualified for the round of 16 at the World Cup despite being held 1-1 by Iran in World Cup Group B after Cristiano Ronaldo missed a penalty.
The European champions, needing a draw to qualify, went ahead with a stunning Ricardo Quaresma goal in the 45th minute.
Ronaldo had a chance to extend the lead when he won a penalty in the 51st minute but Iran goalkeeper Alireza Beiranvand dived to his left to save his effort from the spot.
Karim Ansarifard equalised with a stoppage time penalty awarded after a video review. However, Portugal clung on to finish second in the group with five points behind Spain who will meet Uruguay in the knockout stage.
Uruguay 3 - 0 Russia
Uruguay burnished their World Cup credentials with a 3-0 victory over 10-man Russia, finishing top of Group A with a perfect record while dampening the hopes of the tournament hosts, who had to settle for second.
Luis Suarez grabbed his second goal of the tournament to open Uruguay's account with a free kick after 10 minutes and they doubled the lead with an own goal from Russia's Denis Cheryshev soon after.
That silenced a vociferous home crowd who had been in party mode after Russia's opening two victories and were not expecting their final group contest to be effectively ended in the 36th minute when Igor Smolnikov was sent off for a second booking.
Luis Suarez celebrates after scoring the opener by free kick in the first half during the match of the first stage Source: AAP
Edinson Cavani bundled home a third goal for Uruguay at the death to wrap up their third straight victory, ensuring they finished above the Russians, who will now have to face the winners of Group B Spain in the last 16.
Uruguay, who kept their sixth straight clean sheet, will face Portugal.
While Russia had confounded those who predicted a group stage exit with resounding victories over Saudi Arabia and Egypt, there was still a question mark over how they would perform when they faced stronger opposition.
Saudi Arabia 2 - 1 Egypt
Saudi Arabia managed their first win at the 2018 World Cup by beating Egypt 2-1 with a last-gasp winner that eclipsed Egyptian talisman Mohamed Salah's 22nd minute goal in Monday's Group A game between the two eliminated teams.
Saudi Arabia finished third in the group standings, scoring their only goals of the tournament and vastly improving from the thrashing by hosts Russia.
It was a bitter disappointment for the Egyptian side, however, with Liverpool striker Salah unable to prevent three consecutive defeats for his country. Egyptian keeper Essam El-Hadary became the oldest player ever to appear at a World Cup at 45-years-old.
What matches are next
Socceroos v Peru 12am AEST Wednesday
France v Denmark 12am AEST Wednesday
Argentina v Nigeria 4am AEST Wednesday
Croatia v Iceland 4am AEST Wednesday
The Socceroos need to beat 11th-ranked Peru in Sochi and hope that France defeat Denmark at the same time to have a chance of reaching the last 16.
The Socceroos' fate may be out of their hands -- and goal difference may ultimately deny them -- but coach Bert Van Marwijk is convinced that the seas will part for them.
"I hope and I think that we will stay here in Kazan," a relaxed Van Marwijk told reporters in the changing room at the team's training base.
"I think the players of France they also have their own pride, they won two times but they didn’t play well and they want to prove to the whole world that they are one of the best teams.
"I think so, I believe that they will do their utmost best."
Argentina, bottom of Group D, need victory to progress to the knockout stages and must also hope Iceland do not beat Croatia, because that could send them out anyway, depending on goal difference.
Nigeria, second in the group, will advance if they beat Argentina, while a draw may also prove to be enough even if third-placed Iceland beat Croatia.
The match may be Messi's last at a World Cup if his team do not escape their group. The 31-year-old has so far struggled to make an impact, missing a penalty in the 1-1 draw with Iceland and being marked out of the game in the emphatic 3-0 defeat by Croatia.
"We love this great player Messi, everybody loves him. But the question for us is not if it's the last World Cup for him," Nigeria coach Gernot Rohr told reporters on Monday.
"We are not here to watch him play. We're here to get a result. We are professionals and we have to defend the colours of Nigeria. In football there is no mercy, no pity. Everybody wants to win."
