A 93rd minute strike from Fernando Amorebieta puts Boro's Spanish manager, once Mourinho's assistant at Real Madrid, in pole position to take them into club football's most lucrative game -- a playoff final at Wembley offering a passport to the top flight worth over 120 million pounds ($185.46 million).
A calamitous mistake by the visitors' dithering keeper Dimi Konstantopoulos had revived Brentford's hopes at Griffin Park as it allowed Andre Gray to slot home a 53rd minute equaliser.
Earlier, the home fans were largely silenced by a typically efficient performance from favourites Middlesbrough, who had defended stoutly and then struck through Belgian striker Jelle Vossen who, totally unmarked, headed home in the 26th minute.
Karanka, watched in the stands by Chelsea manager Mourinho, appeared to have been lifting a page from the master's book as Boro, unspectacular but composed, appeared largely in control.
The pair, who spent three years as a management team at Madrid, could soon find themselves as rivals in west London if Karanka, who also played for Real, can steer Boro back into the Premier League to have a crack at the champions.
One mistake had threatened to ruin Karanka's night as Konstantopoulos hesitated on the edge of his box, failed to make a clearance and allowed Gray to dart in, block the ball and then turn and slot it into an empty net from an acute angle.
Brentford pressed hard but to no avail until substitute Amorebieta swivelled to convert a volley in the dying seconds.
Afterwards, Karanka insisted to reporters that the job was only half-done. "You know it's always important to win the games, especially away, but we didn't do anything yet because Brentford are a very good team," he said.
With the second leg to come at Middlesbrough's Riverside Stadium next Friday, Brentford, who had finished seven points behind fourth-placed Middlesbrough in fifth, now have their work cut out to reach the top flight for the first time since 1947.
The first leg of the eagerly-anticipated second semi-final between East Anglian rivals Ipswich Town and Norwich City takes place at Portman Road on Saturday, with the return a week later.
($1 = 0.6470 pounds)
(Writing by Ian Chadband; Editing by Ken Ferris)
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