Madrid in worst start in 10 years, Barca stay top
Real are also eight points behind rivals Barcelona who won 4-1 at Getafe to retain their 100 percent record.
Trochowski grabbed the winner when the German international was quickest to react to a corner after just two minutes.
Cristiano Ronaldo, who was the centre of attention in the build-up to the game after claiming he was unhappy in the Spanish capital, produced two saves from Andres Palop on 10 minutes and another from a tight angle before half-time.
Jesus Navas and Cicinho combined well on the right, and with Alvaro Negredo bravely leading the attack for Sevilla, the home side always looked dangerous on the counter-attack.
Mourinho showed his discontent by ordering his substitutes to warm-up on the half-hour mark.
Luka Modric and Karim Benzema replaced Angel Di Maria and Mesut Ozil at the interval in an attempt to change the game.
The summer signing from Tottenham, Modric, produced a spectacular save from Palop on 52 minutes, but a minute later Negredo should have doubled Sevilla's lead.
Sergio Ramos then headed a difficult ball over the bar from almost on the goal-line and with 25 minutes remaining Mourinho made his final change replacing Alvaro Arbeloa with Jose Callejon.
Fernando Navarro made a brilliant last gasp tackle to deny Ronaldo whose face failed to hide his frustration.
Barcelona made it four wins in four games with a 4-1 victory at Getafe.
Brazilian full-back Adriano grabbed an early lead for Barca before Lionel Messi left the bench to grab a double, to make it six league goals for him, and assure the points for the Catalan side.
Pablo Sarabia got a late consolation for the home side before the recovering David Villa also came off the bench to claim his second of the season.
Barca coach Tito Vilanova was happy with the result but concerned about Carles Puyol who limped off in the second-half, just four days before the visit of Spartak Moscow in their opening Champions League fixture.
"The most important thing is we have 12 points from 12, we tried to control the game and we could have scored a few more. We'll see tomorrow how long Puyol will be out, it's a problem, he gives us a lot of organisation at the back and is very important for us," said the coach.
Vilanova decided to rest Messi, leaving the Argentinian to start from the bench for the first time in just over a year.
Cesc Fabregas made a probing run from deep on 32 minutes before stabbing the ball into the path of Adriano who needed only one touch to grab his second goal in two games for the opener.
Messi appeared with 30 minutes remaining to slot home a penalty on 74 minutes after Juan Valera had tripped Pedro Rodriguez.
Four minutes later, Messi was on hand to finish a cross from Martin Montoya before Villa rounded-off a straightforward victory.
Malaga beat Levante 3-1 to record their best ever start to a La Liga season with 10 points from four games to stay two points behind Barca in second position.
New signing, and former Real Madrid forward, Javier Saviola was the instigator with the first goal before providing an assist for Joaquin Sanchez, either side of the break.
Michel had pulled Levante level just after the interval but Malaga deserved the victory and youngster Francisco Portillo rounded of the scoring in the last minute.
French international full-back Aly Cissokho starred as Valencia beat Celta Vigo 2-1 to record their first win of the season.