Tony Pulis’s side returned to winning ways with a routine win at the Riverside, after suffering their first defeat of the season at Norwich last weekend.
Pulis opted to ring the changes in the wake of Saturday’s setback in Norfolk, switching to a flat back four instead of the five-man defence he had been fielding in recent games.
The Boro boss also handed Jordan Hugill a first league start in place of Assombalonga, and the hosts spent most of the first half trying to feed the ball in to the West Ham loanee.
Hugill thought he should have had a penalty when he went down under a challenge from Mark Beevers, then Jonny Howson twisted past his marker before firing over from 25 yards.
Even so, Bolton were holding out reasonably well before an error from former Middlesbrough midfielder Gary O’Neil undid all their good work.
Stewart Downing’s long-range strike was blocked, but O’Neil attempted a dreadful pass to his own goalkeeper which instead struck David Wheater.
The ball broke kindly for Saville and the summer signing swept home his first goal since he joined on loan from Millwall in the summer.
Ben Alnwick dened Ryan Shotton after a low strike, while Martin Braithwaite whistled another effort over the crossbar.
Former Middlesbrough full-back Jonathan Grounds saw his drive sail over the crossbar.
That was a difficult opportunity, but the visitors spurned a much better one on the hour mark.
Grounds’s deflected shot fell nicely for Josh Vela, but the striker could only direct a tame side-footed effort straight at goalkeeper Darren Randolph when he should really have scored.
Assombalonga came off the bench late on, and when Marc Wilson failed to deal with a late long ball, the substitute galloped clear to score and secure all three points.
Middlesbrough: Randolph, Shotton, Ayala, Flint, Friend, Howson, Clayton, Saville (Besic 78), Downing (McQueen 74), Hugill, Braithwaite (Assombalonga 76). Unused substitutes: Batth, Konstantopoulos, McNair, Fry.
Bolton: Alnwick, Olkowski, Hobbs (Wilson 33), Wheater, Beevers, Grounds (Wildschut 78), Joe Williams, Lowe, O’Neil, Magennis, Vela (Oztumer 65). Unused substitutes: Little, Donaldson, Noone, Matthews.
Referee: D Coote (Notts).