A second-half double from Scott McDonald ensured that Wanderers returned from their first trip to the Riverside Stadium in four years with nothing to show for their efforts.
Things had been looking good for Bolton at the break as they went in with a 1-0 lead through Chung-Yong’s first goal since April 2011.
But strikes from Middlesbrough’s Australian striker – a tap-in on 66 minutes and a close-range header five minutes before full-time – decided the game in the home side’s favour.
Jimmy Phillips shuffled his pack ahead of his last game in interim control. Sam Ricketts replaced Matt Mills at centre-half and Chung-Yong was drafted in on the right-side midfield as Benik Afobe dropped down to the bench.
In terms of goalscoring opportunities, Middlesbrough bossed the first half but it was Bolton who took a lead into half-time.
Former West Bromwich Albion striker Ishmael Miller spurned several chances in the opening 45 minutes, the easiest by far being a free header from just five yards out which was glanced wide of the far post.
Miller also curled narrowly over the bar from the edge of the box with his left foot, and flashed an effort across goal and just inches wide of the target.
Adam Bogdan played his part too, tipping Grant Leadbitter’s effort around the post and also beating away a Marvin Emnes shot after Boro had broken clear when Tyrone Mears was guilty of losing possession on halfway.
It was all Boro for the first half an hour with right-winger also Adam Reach wasting two decent opportunities, blazing them both over the crossbar.
However, there was an encouraging end to the first half for Bolton who began to offer much more in the final third and, indeed, notched the deadlock breaking goal.
After Chris Eagles had been booked for diving inside the penalty area and Mark Davies had dragged a 20-yard effort narrowly wide, Chung-Yong got his first goal in a Wanderers shirt for 18 months on 42 minutes.
Eagles’ pass deflected through the Boro defence and the South Korean timed his run to perfection before rounding-off the move with a cool finish into the corner of the net from ten yards out.
Just two minutes later and Chung-Yong once again found himself in the right place as Andre Bikey slipped just outside the Boro area. He was presented with a free run on goal but he could only place his lofted shot over the bar – it proved a costly miss.
Boro came out after half-time and turned the game on its head as Scott McDonald, on for the injured Marvin Emnes, bagged twice to guarantee that it was the home side that recorded all three points.
Bolton felt aggrieved not to have been given the chance to have extended their lead from the penalty spot when Chung-Yong was seemingly barged over by Seb Hines, only for referee Sutton to wave the appeals.
And Eagles too came close following a sprint from halfway and a shot which whistled fractionally past the post.
McDonald was presented with a simple task of converting from five yards for the equaliser.
Ishmael Miller burst down the left and fired towards goal with Bogdan making a neat low save, but the rebound landed right at the feet of the former Celtic striker who made no mistake to level the scores.
It was a fairly even end to the match as both team pressed and probed for the winner, but the only clear-cut chance that was created fell to the home side – and they took it, again through McDonald.
A cross was swung over from the right touchline by Emmanuel Ledesma and McDonald, unmarked, nodded the ball into the bottom corner, leaving Bogdan with no chance.
Bolton went with a three-pronged strikeforce of Kevin Davies, David Ngog and Benik Afobe in the dying minutes, but there was to be no second goal for Wanderers, who were watched from the stands by new manager Dougie Freedman throughout the full game.
Middlesbrough: Steele, Bikey, Friend, Leadbitter, Emnes (McDonald 22), Hines, McEachran (Halliday 87), Parnaby, Reach (Ledesma 46), Miller, Haroun (Subs not used: Leutwiler, Hoyte, Bailey, Smallwood)
Wanderers: Bogdan, Mears (Ngog 87), Ricketts, Ream, Warnock, Chung-Yong, M Davies (Pratley 75), Spearing, Eagles, Petrov (Afobe 65), K Davies (Subs not used: Lynch, Mills, Andrews, Riley)
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