Ryan Giggs scored in the 67th minute from Rooney's pass and Rooney himself netted in the 69th after United had wasted a dozen chances against the unheralded German side.
"We have to say without envy that we never had a grip on the game except for the first 15 minutes," Schalke defender Christoph Metzelder said. "We were clearly outplayed."
Schalke goalkeeper Manuel Neuer made a string of fine saves to keep his team in the match for more than an hour despite strong pressure by United, which now looks set to reach the May 28 final at Wembley against either Real Madrid or Barcelona, barring an upset next week in the second leg at Old Trafford.
Rooney's performance came on the same pitch where he was infamously sent off during the 2006 World Cup in England's quarterfinal loss to Portugal.
Neuer's heroics prevented United from scoring earlier, but in the 67th he was finally beaten.
Rooney held off three Schalke defenders and slipped a perfect through ball to Giggs, who slotted the ball between Neuer's legs.
Two minutes later, Javier Hernandez was allowed to run unchallenged to the edge of the area and pass to Rooney, who drove past Neuer inside the near post with a low shot.
"I think we showed too much respect from the start," said Neuer, whose team had knocked out title holder Inter Milan in the quarterfinals. "We had trouble winning the ball and did not defend well."
United is seeking its fourth title in the competition, while Schalke is in its first semifinal. Schalke had been unbeaten at home until the semifinal, while United still has to concede a goal away from home.
The Red Devils previously went out four times against German opposition — in the semifinals against Borussia Dortmund (1997) and Bayer Leverkusen (2002), and twice against Bayern Munich in the quarterfinals (2001 and 2010).
Alex Baumjohann fired the first shot less than a minute into the game after splitting the United defense, but Edwin van der Sar had no trouble catching the ball.
At the other end, Rooney's deflected shot nearly beat Neuer, but instead brought a corner.
Antonio Valencia then fed Hernandez but Neuer was well placed to stop the effort, after earlier parrying a drive by Park Ji-sung.
Fabio had a great solo run and outpaced three Schalke defenders but ran out of steam before threatening Neuer.
In the 14th, Hernandez beat the offside trap but could not beat Neuer as the Schalke goalkeeper somehow scooped the ball.
Hernandez shot wide in the 21st, then dispossessed Kyriakos Papadopoulos and swapped passes with Rooney, only to have Joel Matip make a desperate clearance.
Hernandez again came close in the 26th minute but shot wide across the goal from a tight angle.
In the 28th, Neuer made a stunning reflex save from a close-range header from Giggs off a cross from captain Nemanja Vidic.
Hernandez had another effort parried by Neuer in the 37th, Park got the rebound but Atsuto Uchida hurled himself before the South Korean to block the effort.
With the Red Devils dominating late in the first half, Fabio sent a left-foot effort over the crossbar.
Neuer, easily the busiest and arguably the best man on the field, was nearly beaten by Giggs after a counter attack but somehow stuck out his right hand to palm the ball away.
Hernandez did find the net, but he was flagged offside.
One of Schalke's rare forays outside its half finished with Jose Manuel Jurado's mistimed volley off a cross from Jefferson Farfan.
With Schalke shaking off some of the pressure, Raul Gonzalez sent a useful cross to the far post but the United defense rose to the task.
Edu then tested Van der Sar, who smothered the ball in the 65th. But United responded with two quick goals and then cruised until the final whistle.