John Terry's deflected close-range effort beat Hugo Lloris to put Chelsea ahead at the end of the first half and Kyle Walker turned Diego Costa's low drive into his own net after the break to give Mourinho victory in the pouring rain.
Both goals were slightly fortuitous - but few would argue the Chelsea boss was lucky to win the trophy on Sunday.
Tottenham came to Wembley full of hope after their recent rejuvenation under Mauricio Pochettino
The men in white played some fantastic football - and Christian Eriksen went close to giving them the lead when he struck the bar in the first half - but ultimately he was outwitted by his opposite number.
Shorn of the giant protective presence of Nemanja Matic, the theory was Chelsea's defence would be vulnerable to the threat caused by boy wonder Harry Kane and the tricky Eriksen.
But Kurt Zouma, operating as a defensive midfielder, kept Eriksen quiet all afternoon
It was a masterstroke from Mourinho.
It says much about the Portuguese that his two-and-a-half year wait for a trophy was described as a "drought" in the build-up to this game.
E ven his most damning critic cannot argue he does not deliver on the biggest stage
This was his ninth win in 12 major finals
His 21st trophy has come in just his 15th year in management
That is quite some achievement
The first time he won this cup in 2005, it triggered an avalanche of trophies and he will now hope that is the case again.
At first glance, Mourinho barely looked bothered by the occasion as he waited for the dignitaries pre-match
The Chelsea boss stood with his hands in his pockets, the top button of his shirt undone, his tie loose
But the concentration on his face showed he was taking anything but a casual approach to the match
He was up for it.
Still, he could not prevent Tottenham dominating the opening exchanges.
A 1,500-mile midweek trip to Florence had not sapped Spurs of the energy, dynamism and intensity which have become the hallmarks of Pochettino's team.
Lloris, who started ahead of Michel Vorm, tipped a looping Branislav Ivanovic cross wide, but other than that the Tottenham goalkeeper remained largely untroubled.
Four Chelsea players tried and failed to halt Kane in his tracks as he darted towards goal
Cesc Fabregas stopped the striker in his tracks illegally and Anthony Taylor awarded a free-kick 23 yards out.
Eriksen whipped the set piece over the wall and past Petr Cech - but the ball rattled the bar and bounced to safety.
Spurs pressed Chelsea high up the field and successfully picked holes in their defence.
Danny Rose, Walker and Andros Townsend got in behind - but their final ball was poor.
Tottenham looked the more threatening team, but other than saving a weak Kane shot, Cech had little to do.
Zouma prevented Eriksen from causing havoc
The one time he got past the big Frenchman, Cech was on hand to save at his near post.
Referee Taylor had to work hard to keep a lid on proceedings.
Gary Cahill clattered into Rose shortly after the Spurs left-back had bundled Eden Hazard over.
Costa, who had earlier clashed with Eric Dier, squared up to Nabil Bentaleb after the Algerian reacted to a push in the face from the £32million striker.
Taylor booked Dier for a foul from behind on Costa 10 minutes before the break.
Mourinho, who did not budge from the touchline, saw his team snatch the lead in the final minute of the half.
Nacer Chadli was penalised for a foul on Ivanovic and Willian whipped in the free-kick to the near post
Bentaleb's header fell into Terry's path and he fired past Lloris - after a big deflection off Dier.
The heavens opened during the interval and Spurs could not manage a repeat of their quick start to the first half when play resumed
Despite the presence of three Tottenham players around him, and the slippery surface, Fabregas drew a top-class save from Lloris with an acrobatic effort
A few minutes later, Chelsea had a two-goal cushion
Fabregas slotted the ball into Costa after a well-worked move from the half way line and the Spain striker drove a low shot towards the back post which was accidentally turned past Lloris by Walker's right boot.
Hazard, a constant threat all afternoon, almost got the goal his performance deserved in the dying minutes.
Mourinho brought Didier Drogba on in the closing stages for what could be his last Wembley hurrah for the Blues.
And the Portuguese revelled in the glory as the Chelsea fans chanted his name at the final whistle.
Source : PA
Source: PA