A terrific Lewis Sirrell strike from 22 yards brought a smart save from Jon Flatt in the game's first attack with five minutes played.
Eusebio Bancessi set off on a determined run in the Boro half and set up Anthony Forde in a break which almost brought a goal a few minutes later. Forde's cross struck Jim Kellerman and Luke Coddington produced a smart save.
The touch from Bryn Morris was slightly too heavy when he tried to set up Bradley Fewster and it was the visitors who crafted two chances down the right, the best of which ought to have been converted.
Forde and Bancessi had switched flanks and it was Forde, now on the right, who sent over a good cross which Jim Kellerman headed wide, much to his obvious frustration.
When Hines fouled Kellerman on the edge of the penalty area Wolves were in with a chance of breaking the deadlock, but Forde's shot was struck low into the wall.
A snap-shot from Jones was blocked before Flatt had to work, although the goalkeeper was called into action with 33 minutes played when the same player shot from the edge of the box.
A Forde corner fell perfectly for Liam McAlinden a couple of mitnutes later and although the striker made reasonable contact the shot was comfortably cleared.
Another corner on 41 minutes wasn't deal with and from it Wolves took the lead as Jamie Tank was the strongest in a clutch of players challenging, his powerful header from seven yards giving Coddington no chance.
Half-time: Boro U21s 0 Wolves U21s 1
As he had in the first half, Sirrell also had the first chance of the second but he shot wide from close to the edge of the penalty area.
Wolves went within a whisker of adding a second with their first corner of the second half. A left-wing delivery was cleared but left-back Jordan Cranston took control and struck a low shot from 22 yards against Coddington's right-hand post.
That signalled the start of a small period of Wolves pressure but the closest they went to adding the to their lead was a when left with a two-on-one advantage but Kellerman shot off target with McAlinden better placed to his right.
Hesitancy in the Wolves defence allowed Fewster a chance from a difficult angle and although he was well off target, he was the one who had created the chance.
Charlie Wyke added a presence to the forward line when he was introduced just short of the hour-mark, but despite added possession Boro found it difficult get through to Flatt.
Chances were limited at both ends but with two minutes of the game remaining Wolves had a chance to add a second when Coddington couldn't hold a low, 20-yard drive from Forde and for a moment it looked as though the ball was going to fall for David Moli but Boro's defence reacted quickly.
However, the visitors wrapped up the win with a fine goal in the first minute of injury-time when Anthony Forde curled a delightful shot over Coddington from 20 yards.
Boro: Coddington; Bennett, Hines (Burn 71), Jackson (Capt), Meling, B Halliday, Sirrell, Morris (Wyke 58), Fewster (Kneeshaw 78), Park, Jones. Unused subs: Fryer (gk); Waters.
Wolves: Flatt; Kostrna, Cranston, Whittall, Ihiekwe, Tank, Bancessi (Parry 63), Jakobsson, McAlinden (Carter 90+1), Kellerman (Moli 75), Forde. Unused subs: Dutton, Iorfa.