John Deacey cited horses for courses as he made a handful of changes to the side, the Boro boss knowing that it would be nothing more than a battle on the banks of the River Mersey.
Boro looked bright throughout the first half, but they were punished once for over-extending once and Warrington went in at the break with a 1-0 lead.
James Walshaw was Boro's main threat in the first few minutes.
The club's top scorer spun well 35 yards from goal, but had his lofted effort well gathered by Tony McMillan.
Then Walshaw charged clear on the left, but having drilled past McMillan, his shot was cleared off the line by an alert defender.
Fighting for the solitary promotion spot, Warrington certainly had the credentials to cause problems, and burly attacker Josh Amis hit the post with a header, then seconds later, David Raven scuffed horribly wide when through on keeper Tommy Taylor.
It was the Yellows who took the lead on the half-hour when Boro over-committed in attack and were caught on the counter.
Luke Dean gave the ball away and missed a tackle, before the ball flowed into the path of the experienced Tony Gray, who outpaced Josh Lacey and bent past Taylor and into the net.
Boro almost replied instantly, but Michael Coulson's goalbound shot struck fellow attacker Walshaw and rolled out for a goal-kick.
The keepers exchanged useful saves after this, with McMillan palming away a towering Bailey Gooda header, before Taylor got down well to frustrate Mark Roberts.
Taylor was at it again minutes after the resumption, springing across his goal to push away a Gray curler.
The bench sprang into action as things began to go stale, with Jack Johnson, Luke Lofts and Flynn McNaughton giving things a more attacking feel.
With the reshuffle bedded in, Boro began to make the opportunities to level things up.
McNaughton outmuscled the full-back, but saw his effort well saved.
Then Walshaw attempted a spectacular overhead-kick that spun just wide.
Boro also had a good penalty shout when Coulson was manhandled in the box, but much to the travelling fans' frustrations, the ref was having none of it.
With Boro pushing and pushing, it was Warrington who managed to score the second of the game. On the counter, Jack Dunn prodded home from close range to double the lead and smash any lingering hopes of a play-off place for the men from the Flamingo Land Stadium.