The Frenchman, who kept his side in the FA Cup with a last-gasp equaliser at Wycombe on Tuesday night, produced a smart finish again to clinch a 2-1 victory at chilly Craven Cottage and leave Steve McClaren nervously scrutinising the league table.
Boro centre-back Colin Cooper took advantage of an awful defensive mix-up between Cottagers goalkeeper Edwin van der Sar and midfielder Sylvain Legwinski to nod home a soft eighth-minute opening goal.
But Jean Tigana's side established their slick passing game and substitute Louis Saha needed just five minutes on the pitch to power home a great diving header for the 40th-minute equaliser.
Saha then turned provider to slip a pass through to Marlet - nearing full fitness after a two-month injury lay-off - who tucked the ball under Mark Crossley for his third goal in four games on the stroke of half-time.
After the interval, Fulham came close to extending their advantage over shot-shy Boro - but will be happy to record a 2-1 success which cements their position in mid-table.
Cottagers winger Luis Boa Morte was ruled out by a one-match suspension, while struggling Boro - whose league win against Everton and FA Cup draw at Wimbledon had ended a run of four straight defeats - were without forward Alen Boksic, sidelined with a calf strain.
Argentinian midfielder Carlos Marinelli returned for the visitors after overcoming an ankle injury - and Boro raced into an eighth-minute lead after his hopeful free-kick resulted in a terrible defensive mix-up between Fulham keeper van der Sar and Legwinski.
The Dutch shot-stopper inexplicably left the ball to go out of play at the far post, just as Legwinski allowed Cooper to have a yard of space to nod the ball into the net for one of the softest goals of the season.
Fulham attempted to hit back when Steed Malbranque slipped a great pass through to Marlet - but Crossley deflected the Frenchman's shot skywards and Hayles headed the loose ball just over the crossbar.
Marlet came closer than his strike partner Hayles after 23 minutes. Legwinski humped a hopeful cross into the box and the former Lyon frontman rose highest to plant a firm header just inches over Crossley's bar.
Collins curled a 20-yard free-kick a foot wide of Crossley's left-hand post before Fulham manager Jean Tigana made an attack-minded substitution after 35 minutes.
Off came Legwinski, suffering from what appeared to be a thigh injury, to be replaced by forward Saha.
Hayles brought a spectacular save from Crossley a minute later with a powerful header from a dinked Steve Finnan cross.
And at the other end, Paul Ince's deflected long-range shot and Noel Whelan's back-header were both comfortably gathered by van der Sar.
The equaliser the home side deserved finally arrived in the 40th minute, when Saha rocketed a diving header past Crossley from a precise Malbranque free-kick.
And it got even better for Fulham in stoppage time as Saha's poked ball into the box was deflected into the path of Marlet, who cleverly tucked it under Crossley to make the half-time score 2-1.
At the start of the second period, Marlet flashed a header a yard wide of Crossley's goal as the Cottagers tried to extend their lead.
And Tigana's team were agonisingly close to establishing a two-goal cushion in the 63rd minute. Saha's towering header was deflected goalwards by Marlet - but
Robbie Mustoe awkwardly blocked on the goal-line and the ball was scrambled clear.
Play then switched to the opposite goalmouth and Whelan skinned Andy Melville but dragged his angled shot a foot wide of the far post.
Van der Sar gathered Phil Stamp's 20-yard free-kick in the 76th minute and Malbranque came close to adding Fulham's third when Crossley produced a brilliant tip-over from his 15-yard drive late on.