Tony Mowbray named a strong starting line-up, with a potent strikeforce of Leroy Lita and Scott McDonald, with Jonathan Franks and Tarmo Kink given the job of supplying the ammunition.
There was an eight-strong band of Boro fans among the small crowd as the game kicked off in warm sunshine on a decent playing surface.
Boro's first opening came on 10 minutes when Rhys WIlliams, playing in central midfield, sent a long ball through the middle and McDonald made the keeper get down low to save.
Seconds later Kink tested Denis Krklec again with a trademark drive from distance but the shot was plum centre of the keeper's goal.
Boro took the lead on 12 minutes when a driving run from Williams took him into a dangerous area. When he was tackled he managed to stick out a leg and steer the ball towards McDonald.
However, it was defender Simek Karlo who rected first - but only to send the ball into the corner of his own goal from eight yards out.
The Teessiders had the ball in the back of the net again moments later but Lita was marginally offside.
A free-kick routine brought Varazdin's first decent opening after 17 minutes following a foul by Jonathan Grounds.
However, Danny Coyne dived to his left to make a fine save from Nikola Safaric, holding onto the ball well.
Another free-kick just before the 25-minute mark saw Kink do his job in the wall after a Williams foul, before Lita skilfully brought the ball away to safety.
Coyne was called into action again when Kink stopped claiming offside as Varazdin broke.
The Welsh international saved bravely at the feet of Safaric when he looked the favourite to score.
Boro went 2-0 up on 28 minutes when Jonathan Franks did well before releasing Justin Hoyte on the right flank.
The defender skiped past a challenge as he collected the ball, drove to the byline and crossed for Leroy Lita to prod the ball in from close range.
But the home side were given hope with 30 minutes on the clock when Coyne was very harshly judged to have brought down profilic scorer Davor Vugrinec - in fact he had timed his challenge to perfection as the striker hurtled into the box.
Vugrinec - who needs just five more goals to become the Croatian league's all-time top scorer - cooly slotted the ball to Coyne's right as the goalkeeper dived to his left.
The excellent Williams, who was controlling the game from his central midfield position, was not too far off with a long shot that whistled over the bar. 
Then it took a fine tip-over from Krklec to deny McDonald a headed goal from a Franks cross just before half-time.
At the other end Coyne showed his agility as he got down to deny Dejan Glavica at his near post from a tight angle, turning the ball round for a corner.
Half-time: NK Varazdin 1 Boro 2
It took a much-changed Varazdin only seven minutes to level after the teams came out for the second half.
Sub Mario Sacer latched onto a loose ball and let fly with a sizzling shot that beat Coyne but hit the post before rebounding across the goal and to what looked like safety.
However, Marko Trojak had other ideas and showed composure and control to steer the ball firmly in from a tight angle.
But captain Matthew Bates showed similar qualities on 79 minutes to give Boro the lead once again.
The move was started off by Tony McMahon and then Bates exchanged a clever one-two with Lee Miller. The second pass lifted the ball over the remaining defenders and left with the task of beating the goalkeeper, Bates simply lifted it over his head and into the roof of the net, despite the best efforts of a defender.
Bates had earlier been booked for a foul.
McMahon came close to adding a fourth on 84 minutes after another move he started himself. Miller again did well in the build-up to feed Luke Williams on the right, and the Teesville-born forward calmly passed back to the onrushing McMahon.
However, the shot flashed across the face of the goal and wide.
By now Boro were dominating, with a very young Varazdin line-up remaining on the pitch, and when the hosts did break away, the handling of Connor Ripley, on for Coyne for the last 25 minutes, was safe and secure.
NK Varazdin: Krklec, Tkalcic, Conjar, Susac, Simek, Safaric, Brlecic, Glavina, Vugrinec. Subs: Mrmic, Antolic, Loncar, Gluhak, Kaniski, Kukec, Grgec, Trojak, Cerovecki, Golubar, Sacer, Medved, Pajac.
Boro: Coyne (Ripley 65), Hoyte (McMahon 65), Grounds (Bennett 65), Bates, Williams R (Martin 60), McManus, McDonald (Miller 73), Bailey (Smallwood 60), Lita (Main 73), Franks (Williams L 60), Kink (Reach 60).
Man of the Match: Rhys Williams
