Matty Dolan, Ryan Brobbel and Bradley Halliday were added to the U21 side that lost to Leicester City at Hartlepool on Monday, replacing Adam Reach, who was starting his loan spell with Shrewsbury Town, Cameron Park, who was injured, and Andre Bennett, who dropped to the bench.
As against Leicester, Boro started the game well and an impudent piece of skill by Brobbel after just six minutes saw him race clear down the left, but his shot was saved by Bettinelli.
Two minutes later a fantastic reaction save from Boro keeper Luke Coddington denied Passley's point-blank header from a Kavanagh free-kick.
On 24 minutes Tankovic played in Richards, who looked to have struck a goalbound shot but Boro captain Adam Jackson appeared from nowhere to block.
Play was moving from end to end now as chances were starting to be created. Luke Williams found himself one-on-one but Bettinelli was out swiftly to smother the danger.
It was then Fulham's turn to attack and on 29 minutes a right-wing cross from Richards nearly forced Bradley Halliday to slice the ball into his own net, but fortunately it went just wide of the post.
On the stroke of half-time Boro had what was the best chance of the game so far when a quick break ended with a three-to-one advantage. However, the visitors failed to capitalise as Andy Halliday's left-foot curler cleared the upright.
Half time: Fulham U21s 0 Middlesbrough U21s 0
Boro nearly broke the deadlock on 48 minutes when Andy Halliday picked the ball up 20 yards out but his thumping left-foot shot smashed against the crossbar and was cleared to safety.
Fulham took the lead after 52 minutes through a truly sensational strike from full-back Brister. A long ball found him on the far right-hand side of the penalty area. He then took a touch and with the outside of his right boot bent the ball into the top corner of the net.
The home side were now brimming with confidence and Coddington again made a smart stop to deny Trotta after he was found by Brister.
Still Fulham pressed and after 58 minutes Boro centre-half Jonathan Burn produced a brave block to stop Trotta's progress.
Entering the final 20 minutes Boro started to pile on the pressure in a bid to gain the equaliser. Andy Halliday tested the keeper after 70 minutes and substitute Wilson Kneeshaw was crowded out just minutes later.
On 83 minutes Jordan Jones, who had looked very impressive having come on as sub a few minutes earlier, had a right-foot shot that flew agonisingly wide of the target.
Andy Halliday had another chance but his header from a Birger Meling cross cleared the bar.
Jones then went on a trademark jinking run but was brought down on the edge of the box. Dolan stepped up and it looked a goal as soon as it left his foot but somehow it went millimetres wide.
The final action of the game came when Jones saw his effort from range tipped wide of the target.
Scorer: Brister 52
Fulham: Bettinelli, Brister, Kavanagh, Christensen, Arthurworrey, Grimmer (Capt), Passley, David (Minkwitz 77), Trotta (Islamovic 81), Tankovic (Woodrow 62), Richards. Unused subs: Joronen (GK), Buatu
Middlesbrough: Coddington; B Halliday, Burn, Jackson (Capt), Meling, Dolan, Brobbel, Morris (Bennett 83), Williams (Jones 76), Waters (Kneeshaw 62), A Halliday. Unused subs: Fryer (GK), Weledji
Referee: John Busby
Boro Man of the Match: Impressive performances from Brobbel and substitute Jones but the award goes to goalkeeper Luke Coddington. Fresh from his England U19 call-up, he took this into the game and produced some excellent saves in an assured display.