The Blues again led at half-time, on Tuesday night, but suffered more second-half agony.
Former Scarborough Athletic striker Jake Charles chipped home a superb solo effort to put Whitby ahead, eight minutes before half-time.
However, hosts Hebburn levelled moments into the second-half.
A penalty for a push from Connor Smith then enabled the Tynesiders to lead for the first time.
They made sure with a late third to go top of NPL Premier.
Blues player-boss Gary Liddle told Whitby Town TV it was no more than his side deserved and resembled the 2-1 weekend loss at Prescot:
" Very much like Saturday, we went in a goal to the good with something to hold onto.
"And you say all the right things at half-time and hope the lads have learned lessons from the weekend, but within 30 seconds to a minute after the restart, you're conceding. And then obviously the game's not done by then, but the goals that followed that, goals two and three, were just as bad in decision-making, desire, fight, all those things, come into question. Because it was a game for that tonight, where just playing the percentages and playing the basics of football, especially on a really difficult pitch and all the stuff that Hebburn are really good at.
"We needed to match that tonight and didn't quite do that. And as I said, deserved winners on the night were Hebburn Town."
Whitby return to action, at home to Gainsborough Trinity, on Saturday.


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