Trotters boss Gary Megson paid French club Toulouse £10 million ($14.8
million) for the forward in June, but the 27-year-old had failed to score in nine games since notching in the opening match of the season.
However, despite being dropped by Sweden, his stunning strike against Boro will have helped prove his ability to doubting Bolton fans.
The result brought an end to Middlesbrough’s six-game unbeaten run in the English Premier League and meant they dropped three places to 11th.
Meanwhile, Bolton stay 13th but now have a four-point cushion above the relegation zone.
The visitors quickly went 2-0 ahead after Iceland defender Gretar Rafn Steinsson headed in Matthew Taylor’s eighth-minute free kick and set up Taylor to score two minutes later.
Boro’s Emanuel Pogatetz gave the hosts hope with a goal 13 minutes from time but within a minute, Elmander ensured the points for Bolton with an impressive strike.
Megson had named an unchanged side, while Middlesbrough manager Gareth Southgate replaced hamstring injury victim Chris Riggott with David Wheater at centre-half.
Bolton wasted no time in taking the lead.
Pogatetz was booked for chopping down Elmander and from Taylor’s resulting free kick, Steinsson was unmarked at the far post and directed his header over goalkeeper Ross Turnbull.
And Steinsson returned the favour just two minutes later, crossing from the right wing for Taylor, who outfoxed Gary O’Neil before blasting a shot which went in off Turnbull’s right-hand post.
The hosts nearly pulled one back straight away when O’Neil fired a shot through the crowd, but Kevin Nolan booted the effort off the goal-line.
Bolton defended their lead, frustrating Middlesbrough and reducing them to long-range efforts.
Left-winger Stewart Downing, who performed well for England during Wednesday’s 2-1 win over Germany in Berlin, had a shot from distance but Bolton’s Finland goalkeeper Jussi Jaaskelainen easily saved it.
Boro emerged from the half-time break in determined mood and Tuncay went close with two opportunities as Bolton let the hosts dominate possession.
Middlesbrough did manage to pull one back when the Trotters failed to clear the ball following a corner and Austria defender Pogatetz fired an excellent left-foot shot past Jaaskelainen.
However, Elmander swiftly hit back for Bolton, chesting down a Jlloyd Samuel cross and blasting in a left-foot volley past Turnbull.
Gary Cahill cleared another O’Neil effort off the line late on but thanks to Elmander’s quick reply to the Pogatetz goal, Bolton’s three points were secure.