Japan thrashed Syria 5-0 to finish top of their World Cup qualifying group on Tuesday but they needed a flurry of late goals to give the scoreline a flattering complexion.

A freak own goal from Hamdi Al Masri after 17 minutes put Japan in front before Shinji Kagawa scored twice and Syria crumbled in the second half as the home side topped Group E in the second round of qualifying for the 2018 World Cup and 2019 Asian Cup.

Japan finished with 22 points from their eight games -- four more than Syria, who will also advance to the next round as one of the four best-performing group runners-up.

The Blue Samurai scored 27 goals and conceded none from their eight home and away games with Syria, Singapore, Afghanistan and Cambodia.

But they struggled to stamp their authority on a Syria team missing four key players, axed by coach Fajr Ibrahim for breaking a team curfew after last week's 6-0 win over Cambodia.

And Japan survived a scare when Mahmoud Al Mawas smashed a long-range drive against the post, moments before Kagawa's volley on 66 minutes effectively put the game beyond Syria's reach.

Keisuke Honda headed Japan's third with four minutes left but there was still time for Kagawa to stab home his second and for substitute Genki Haraguchi to grab a stoppage-time fifth.

"We played a spectacular match," Japan coach Vahid Halilhodzic told reporters. "It will give us confidence and great strength to take into the final round of qualifiers."

Honda told Japan's NHK Television: "It was a goal to go through qualifying with no goals against so that was satisfying.

"But there are still some things we need to work on. We got caught on the counter several times and stronger opponents will make us pay so we need to be wary of that.

"We don't want to be satisfied with this. All the players need to step up and improve in order for us to keep winning."

Shinji Okazaki, who provided the spark as Japan crushed Afghanistan 5-0 last Thursday, was handed the captain's armband on his 100th international appearance.

But the Leicester City striker failed to add to his tally of 48 international goals, missing an open goal in the early salvos and volleying spectacularly off-target just before the interval.

Ibrahim's decision to drop rebel quartet Ahmad Al Saleh, Alaa Al Shebli, Fahd Al Youssef and Sanharib Melki was a tough one, given Syria's struggles amid their country's violent conflict, which has claimed an estimated 250,000 lives, including several footballers.

But his players produced a courageous display nonetheless and Japan goalkeeper Shusaku Nishikawa needed to produce a string of top saves to preserve his clean sheet.