Peter Beardsley's second-string were edged out in the Premier League Cup on Friday, having taken a two goal lead - and Dave Watson's youngsters also went in front on Saturday.
Elias Sorensen headed home inside the first minute at Little Benton and, although Rovers levelled shortly before the half-hour mark, Newcastle regained the lead three minutes later.
Kelland Watts ran from the half way line and fired home from 20 yards - then five minutes into the second half, Danish teenager Sorensen got his second to make it 3-1.
Watson's side were well on course for their first victory of the season, but Kyle Connell pulled one back then Callum Wright made it 3-3.
And, in added time, Blackburn skipper Hayden Carter gave the visitors all three points.
Newcastle United Under-18s: Otto Huuhtanen, Max Allen, Kieren Aplin (Isaac Gamblin 89), Jack Young, Oisin McEntee, Lewis Cass, Thomas Allan, Kelland Watts, Elias Sorensen, Kurtis Russell, Adam WilsonSubs not used: Dan Langley, Thomas Cole, Deese Kasinga, Ryan Barrett