Adebayor, who joined the Spanish giants on loan from Manchester City for the remainder of the season last week, only replaced Karim Benzema in the 84th minute but in his short time on the pitch had a big influence on the match.
He was the player scythed down by Sergio Sanchez that earned the Sevilla player a second yellow card, and then in stoppage time he chested down Lassana Diarra's cross and thumped a volley into the roof of the net.
Real deal: Emmanuel Adebayor broke his Real Madrid duck against Sevilla in the Copa del Rey semi-final
That was the former Togo captain's first goal for the club and helped secure a 2-0 win on the night - Mesut Ozil having put the Spanish giants ahead in the 82nd minute - and a 3-0 win on aggregate.
In terms of the landmark goal, Adebayor joints greats from the club's history. Jose Giralt scored the first goal for Real Madrid in 1903 against Espanyol, the 1,000th was scored by Belmar, the 2,000th by Francisco Gento, the 3,000th Juanito and 4,000th Amavisca.
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Adebayor, who made his first appearance for Madrid in Sunday's league defeat at Osasuna, said: 'It was a special game for me because I love this club and I've always dreamed of playing here. I made my debut at the Santiago Bernabeu and was able to score, so I'm very happy.'
Adebayor also praised the performance of the man he replaced on the night, Benzema, who had a number of decent openings to score himself - none better than in the fifth minute when he missed an open goal after Angel Di Maria's shot had come back off a post - but failed to find the back of the net.
Benzema has found himself under the spotlight after struggling to impress during his time at the Bernabeu but he has started to become more influential in recent weeks.
'I think Benzema played very well. He had several opportunities. He didn't sore, but that's football. He's a good player and he will score many goals at this club,' said Adebayor.
Madrid's success against holders Sevilla means they will now face arch rivals Barca in the final on April 20, with Pep Guardiola's side cruising through their semi-final with an 8-0 aggregate win over Almeria.
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That encounter will be the first time the two Spanish superpowers have met in a final since 1990, when Barca won 2-0 in Valencia.
When asked about reaching a final in his first full week at the club, Adebayor said on his club's website: 'We are going to be facing one of the best teams in the world; it's going to be tough but we will have our chances.
'There's still a long time to go until then and now we need to focus on the league.'
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Explore more:People: Mesut Ozil, Karim Benzema, Sergio Sanchez, Emmanuel Adebayor, Lassana Diarra Places: Madrid, Barcelona