The Socceroos needed a late strike to kick off their Asian Zone Group D campaign with victory at home to Thailand last week, but were much more convincing in Dammam on Tuesday.
Joshua Kennedy was the hero for the visitors, bagging the opener on 40 minutes before adding a second 11 minutes into the second half.
The Saudis, coached by former Barcelona boss Frank Rijkaard, were hugely unconvincing throughout but managed to pull one back from the penalty spot after 65 minutes, Nassir Al Shamrani tucking the ball home.
But the Australians, who won despite keeping star man Tim Cahill on the bench until the 86th minute, wrapped up the points when Luke Wilkshire slotted home a penalty 13 minutes from time.
Elsewhere in Group D, Thailand ran out 3-0 winners at home to Oman.
Sompong Soleb fired the hosts ahead in the 35th minute and Teerasil Dangda made it 2-0 six minutes later. Rashid al Farsi's late own goal compounded Oman's misery.
Japan and Uzbekistan both moved onto four points in Group C after playing out a 1-1 draw in Tashkent.
Server Djeparov opened the scoring for the hosts inside 10 minutes but Shinji Okazaki's 64th-minute header ensured it ended honours even.
In the day's other Group C encounter, North Korea defeated Tajikistan 1-0 thanks to Pak Nam-chol's 14th-minute effort.
Jordan moved into the driving seat in Group A after making it two wins from two with a 2-1 victory over China.
Baha Abdul Rahman (49) hit the opener for the hosts and Amer Deeb (55) made it two. Hao Junmin replied for China two minutes later but Jordan held on for the points.
Iraq struck twice after the break to earn a 2-0 win away to Singapore in the other Group A clash.
The Iraqis, who opened their qualifying campaign with defeat to Jordan, picked up their first points thanks to goals by Alaa Abdul-Zahra (50) and Younis Mahmoud (86).
In Group E, Bahrain defeated Indonesia 2-0 in a game delayed by 15 minutes due to spectators releasing fireworks and flares inside the stadium.
Visitors Bahrain took the lead through Sayed Dhiya Saeed just before the break while Ismaeel Abdullatif added the second 19 minutes from time.
That was the cue for a renewed firework assault by the home fans, forcing the players from the pitch. Order was restored, however, and the rest of the match passed without further incident.
In the other Group E game, Qatar and Iran played out a 1-1 draw in Doha. Hadi Aghili put the visitors ahead a minute into the second half but the hosts sealed a point when Mohamed El Sayed levelled after 56 minutes.
In Group B, Lebanon posted a 3-1 win over the United Arab Emirates after recovering from going behind to a 15th-minute Mahmoud Al Hammadi strike.
Lebanon lost 6-0 to South Korea in their opening qualifier and appeared set for more misery, but an inspired fightback began when Mohamed Ghadar fired home from the penalty spot eight minutes before the break.
Akram Moghrabi fired the hosts ahead seven minutes after the restart before Roda Antar made it three inside the final 10 minutes.
In the other Group B clash, South Korea failed to follow up their mauling of Lebanon as they were held to a 1-1 draw away to Kuwait.
Arsenal new boy Park Chu-young, who bagged a hat-trick against Lebanon, opened the scoring after eight minutes, but Kuwait fought back and found the equaliser through Hussain Ali in the 53rd minute.
Match Report / Reaction