The Gunners scored their goals in a 11-minute period late in the first half through Olivier Giroud, Aaron Ramsey and Mohamed Elneny.
The English giants were held in the second half with the 2014 Asian Champion League winners pulling a goal back off an indirect free kick from Steven Lustica.
Arsenal leave for China winning both games on their first tour to Australia in 40 years after beating A-League champions Sydney FC 2-0 on Thursday.
"They made it quite physical for us, they pushed us a little bit and we played very well for long periods in the first half," Arsenal manager Arsene Wenger said.
"The players who came on in the second half gave us more impetus and we finished strongly, unfortunately we couldn't score any more but overall it was a positive game."
The game drew 83,221 fans for a two-game total of 163,653 for Arsenal's visit.
Arsenal broke away with three goals late in the opening half after a competitive opening.
French striker Giroud swept home a cross from Spaniard Nacho Monreal after an overlapping run on the left in the 33rd minute and they were two-up a few minutes later.
Monreal found Ramsey with a long ball and he lobbed goalkeeper Janjetovic on the edge of the box.
The Gunners grabbed a third goal nearing half-time when Egyptian Elneny's long-range volley deflected off defender Brendan Hamill's leg past Janjetovic into the unguarded net.
Gunners' record signing Frenchman Alexandre Lacazette showed his immense skills when he turned his marker and fired a shot at the keeper in the opening minutes.
Elneny came close to a second goal when another long-range shot cannoned off the underside of the bar wth Janjetovic beaten minutes after the resumption.
But the Wanderers stuck at it and Jack Clisby hit the bar with a drive and Ramsey conceded a free kick with a back pass to substitute goalkeeper Emi Martinez.
Lustica hammered the indirect free kick against Monreal on the goal-line and put the rebound into the roof of the net for his team's opener in the 57th minute.
Wenger made mass changes midway through the second period with Lacazette and Giroud among those substituted.
The Gunners came close to adding to their tally in the final stages with Mesut Ozil and Eddie Nketiah hitting the post and Theo Walcott having a sharp chance saved by goalkeeper Janjetovic.