The Colombo crime family wasn’t the only victim of the GPS tracking device that sparked Thursday’s big mob takedown — it also shook up the New York City bus system.

When MTA mechanics found the tracker during a routine maintenance inspection in November 2016, the Staten Island depot where it was located was evacuated and explosives experts were called in to make sure it wasn’t a small bomb, two sources told The Post.

“It was considered a ‘suspicious package,'” one source said. The Yukon Bus Depot in New Springfield was evacuated for more than two hours “as a precaution.”

The device, which was stuck by magnets to the oil pan under a bus in the middle, quickly turned out to be “just” a GPS — and officials confirmed it hadn’t been installed as part of any official MTA study.

Still, the undercarriage of every bus in the five boroughs was searched for any similar devices using mirrors on metal poles.

“We searched every bus as soon as it happened,” one MTA source said.

The mystery of who might want to track the comings and goings of a Staten Island bus — Terrorists? A disgruntled employee? Some renegade, amateur transit geek? — was quickly solved by the feds.

They tracked the tracker with help from an unlikely source, reputed Colombo capo Joseph Amato Sr. who, amazingly, had reported it lost.

Amato had been keeping tabs on his girlfriend by secretly sticking the GPS on her car for “a period of months,” the feds said in court papers.

“Joseph Amato had purchased the device to place a girlfriend, identified herein as Jane Doe, under close surveillance,” the feds said.

The jealous capo would have to “regularly and covertly retrieve the device, charge it and then reposition it on Jane Doe’s car,” the feds said in the papers, which sought to convince a judge to keep Amato and four other defendants held without bail.

“He abandoned the surveillance only after he discovered that the tracker was no longer attached to Jane Doe’s car, at which time he reported the device lost to the electronic service provider administering the tracking service,” the feds said.

“The device apparently had been discovered and was placed on the MTA bus, likely to thwart Amato’s stalking efforts.”

It didn’t work — Amato promptly bought a new GPS, the feds said.

“Apparently not deterred by the discovery of the first device, in May 2017, Amato obtained a replacement tracking device and again took efforts to place it on Jane Doe’s vehicle and surveil her movements.”

Still, the damage was done: it was upon the discovery of the first tracking device that “the government commenced a larger investigation into Amato,” the feds said.

The FBI investigation, which would loop in the Drug Enforcement Administration and the NYPD, found through wiretaps, search warrants and witness interviews that “the Colombo family is thriving and continues to engage in criminal activity including, among other crimes, acts of explicit violence, extortion, loansharking and the operation of illegal gambling businesses,” the feds wrote.

Twenty defendants have been hit with charges that include racketeering, loansharking and extortion.

Amato faces racketeering charges relating to six alleged victims, two counts of cyberstalking and one count of threatening to commit a crime of violence; he pleaded not guilty Thursday and is being held without bail.