It got even better for the home side just moments later as Fulham defender Tomas Kalas handled in the area which was spotted by referee Martin Atkinson as he awarded a penalty.
Obita put the Royals ahead in the first leg at Craven Cottage on Saturday before Tom Cairney's header left the tie finely poised.
Yann Kermorgant's second half penalty was enough to see Reading through to the playoff final with a 2-1 aggregate advantage.
They will meet either Huddersfield or Sheffield Wednesday on May 29 for the £170m prize of Premier League football next season.
READING FC's goal-scoring hero Yann Kermorgant hailed an "unbelievable" season after he blasted Royals into the play-off final last night (Tuesday). I've been there in my career as a player and go there as a manager - of course it is a different stadium now - but it is fantastic.
But on this occasion he made no mistake, slamming the ball to Fulham goalkeeper Marcus Bettinelli's right to leave Stam's side one win from the big time.
However, Reading were clinging on for the final 20 minutes, with Al Habsi pulling off a stunning save to tip Kevin McDonald's shot over the crossbar and ensure it will be Jaap Stam and the Royals running out at Wembley at the end of the month.
John Swift was the guilty party as he somehow weakly steered Chris Gunter's cross straight at Bettinelli from four yards when it looked easier to score.
"We trained on penalties yesterday and Yann was the only one who scored!"
"It's great to be back at Wembley", said Stam, who won the FA Cup at the stadium with United in 1999. "The players are very happy with him because Ali is a keeper with great reflexes - a terrific game for him".
He is believed to be a top target of Newcastle's but the Fulham manager appears to be of the opinion that none of his star players are leaving. "We were very confident he would score". We are talking about our most important players - they are going to stay with us.
"We know Ali's a great goalie, not only today but all season, that's why he's in goal". They scored one goal, that's it - it's a odd situation.