One of the boys, named locally as Gilbert Collins, aged 15, died at the scene, while his 17-year-old friend was rushed to University Hospital Waterford with serious injuries but died on Thursday afternoon.
Exact details of what happened are unclear but it is understood they were both riding on the same e-scooter when they collided with the coach at around 2am while on their way back from Snap Fitness in the Waterford Retail Park, at Butlerstown North.
There was nobody onboard the JJ Kavanagh coach at the time except the driver, who is understood to be suffering from shock.
The coach company offered its condolences to both families and said it was doing everything possible for their families “at this very difficult time”.
Gardaí appealed for any witnesses to the crash to come forward, especially any road users who may have camera footage (including dash-cam) and were travelling on the Cork road in Waterford city between 1.45am and 2.15am.
Anyone with any information is asked to contact Waterford Garda Station on 051 305300.
Councillor Jason Murphy, mayor of Waterford city and county, said the deaths are a “stark reminder” of the dangers of our roads.
“I didn’t know Gilbert personally but I spoke to the staff at his school, St Paul’s Community School, and they are distraught,” he said.
He said everyone is devastated by what has happened.
“Our sympathy goes to the families of those young boys but also to the driver of the coach.
“This is a stark reminder of what can happen. I would urge everyone to just be extra careful, no matter what mode of transport you use.”
St Saviour’s GAA Club, which is close to where one of the teenagers lived in Ardmore Park, postponed a minis event that was due to take place tonight, due to the deaths.
“Our thoughts and prayers are with the families during this difficult time,” it said in a statement.
Meanwhile, Road Safety Authority CEO Sam Waide has said that Irish roads are unsafe because of an “unprecedented deterioration of behaviours”.
He told the Dáil Public Accounts Committee he cannot make other agencies, such as gardaí, do things that are outside “of our statutory remit”.
Mr Waide said there is “frustration” at the pace of increased enforcement on the roads from gardaí, but added that enforcement is not just the responsibility of the force.
He also called for increased access to technology, such as roadside safety cameras.
His comments come as the death toll on Irish roads rose to 92 with the deaths in Waterford.
“My ask to gardaí is that increased enforcement is sustained going forward into the next three years,” he said.
The RSA’s appearance before the PAC comes against the backdrop of a surge in fatalities and serious injuries on the roads in the last two years.
The committee heard that drink driving is becoming “more normalised”, among other dangerous behaviours on the roads.
Mr Waide said that collective action is needed from the RSA and all relevant parties to reverse these worrying trends.
Fine Gael TD Ciarán Cannon put it to the RSA that part of its current remit, including driving tests and NCTs, is at odds with its road safety remit.
“Do you not see a huge conflict of interest here?” he asked.
“Is it not the case that the more drivers we have on our roads, the more cars we have on our roads, the more income that accrues to the very authority that is responsible for maintaining safety on our roads?”
The RSA boss said the behaviour of drivers on the roads is behind the increasing danger, but the number of vehicles on the roads is “outside of [his] control”.