Judge Brooke Gibson said the boys had not suffered physically or psychologically from the incident, and Mr Wilkie had accepted responsibility for his actions and shown remorse.
He had already suffered professionally from the charges, Judge Gibson said, being made to undertake tasks "which would be seen, in terms of status, as tasks not suited to the role of an inspector".
The incident would also leave "a black spot" on his otherwise untarnished employment record of 32 years.
A police spokesperson confirmed Wilkie had been reassigned to "alternative duties" during the course of the investigation and trial, and would remain in that role pending the outcome of the internal tribunal.
Police Minister Anne Tolley today said the "whole affair is very unfortunate", adding: "It also shows that police don't hesitate to prosecute their own."
However, the ruling was greeted with derision by some, including a protester in court who shouted his displeasure from the public gallery.
As Judge Gibson gave his verdict, the man yelled: "It's an absolute scandal."
Barrister Todd Simmonds said while each case is different, "it is certainly not uncommon for a discharge without conviction to be granted" for a such an offence.
"In my experience a 51-year-old with no previous convictions and an otherwise outstanding reputation would typically be offered diversion for offending of this nature," he said.
"The fact that diversion was not offered to Inspector Wilkie reflects the fact that police officers face particularly close scrutiny and accountability for their actions."
A diversion can be offered to first-time offenders allowing them to avoid a criminal conviction if they apologise.
In court today Judge Gibson acknowledged that fact, saying: "I think it's very likely that if the defendant had not been a police officer he would have been offered a diversion. [But] given his rank I think it is appropriate that a court dealt with the matter."
Wilkie was hugged by emotional family members outside court, but declined to comment to media. His lawyer Richard Earwaker said Wilkie and his family were "very relieved".
"It's been hard for him and his family. He's acted very responsibly right from the start; he obviously is very remorseful, he feels for the young complainants," Mr Earwaker said.
***
Police officers discharged without conviction:
- Sergeant Craig Prior pleaded guilty in April to assaulting a man who claimed to have rifled through his personal cellphone.
- Sergeant Jason Lamont was caught driving nearly one-and-a-half times over the legal alcohol limit in August 2009.
***
FACTBOX:
- Twenty police officers or police staff, of the 115 charged with crimes, have been discharged without conviction since 2009
- Of 23 police officers or staff charged with common assault, five have been convicted and three cases are still in progress
- Of the six police charged with assault with intent to injure, two were convicted
- Of eight police officers or staff charged with careless driving causing death or injury, four were convicted.
