Boro headed to the south coast buoyed by victories over Ipswich and faltering Derby County, but they were brought back down to earth by Eddie Howe's in-form side.
Yann Kermogent opened the scoring from the penalty spot and a screamer from Harry Arter put Bournemouth in command three minutes into the second half.
There was no way back for Aitor Karanka's men, who conceded a third goal when Albert Adomah was harshly adjudged to have fouled Arter and Brett Pitman scored his sixth goal in his last four games from the spot.
Victory for Bournemouth ensured they are a point clear of Watford and Boro with seven games remaining.
Watford had taken over at the summit with a win at struggling Wigan Athletic in midweek, but Richard Chaplow struck deep into stoppage time to end their six-game unbeaten run.
That 95th-minute winner ensured Mick McCarthy's Ipswich move back up to sixth above Brentford and Wolves and level on points with fifth-placed Derby.
Norwich City, who occupy fourth spot, enhanced their chances of securing automatic promotion by beating Nottingham Forest 3-1 at Carrow Road to move just two points behind Watford and Boro.
Brentford are down in seventh and needed two goals in the last five minutes to salvage a 2-2 draw with London rivals Millwall at Griffin Park.
Millwall's failure to hold onto their two-goal lead leaves them seven points adrift of Rotherham United, who sit just a place above the bottom three after suffering a dramatic 3-2 derby defeat at home to Sheffield Wednesday.
Steve Evans' strugglers led 2-1 with three minutes remaining, but stoppage time goals from Atdhe Nuhiu and Kieran Lee stunned the hosts.
There was a sparse crowd at Bloomfield Road as bottom side Blackpool claimed a 1-1 draw against Leeds United, with hundreds of fans boycotting the game in protest against club owners the Oyston family.
Martyn Waghorn's late strike gave Wigan Athletic a 1-1 draw with Lancashire rivals Bolton Wanderers that did little to enhance their chances of staying up, while Nakhi Wells missed two penalties as Fulham won 2-0 at Huddersfield Town.
Brighton and Hove Albion are now 10 points clear of the drop zone following their 1-0 win at Blackburn Rovers, while Charlton Athletic were 3-2 winners over Reading and Cardiff City beat Birmingham City 2-0.
