Kike Sola had wasted a guilt-edged chance to put the hosts ahead with 18 minutes remaining but the game swung in the visitors' favour three minutes later when Ruben Gonzalez was sent off after collecting a second yellow card.
And Valladolid took full advantage as a rapid counter-attack from an Osasuna corner saw Ebert go through on goal and he took his time before chipping the ball beautifully over Andres Fernandez for his second goal in two games.
The German had scored a screamer against Real Sociedad on Monday and he was first to try his luck early on but this time Andres managed to gather at the second attempt.
Osasuna then went onto to enjoy the majority of possession in the first-half but they did not seriously threaten the visitors' goal until after the break when Alvaro Cejudo fired a shot from the edge of the area just wide.
Sola then had his big chance as he weaved a way through several Valladolid defenders on the left side of the area but skewed his shot high and wide when faced with only Dani Gimenez to beat.
Three minutes later the task became even harder for Los Rojillos as Ruben was shown a second yellow card for a very soft foul on Ebert and that was to prove crucial as, with a man less, the hosts were twice opened up on the counter attack.
Ebert failed to beat Andres with his first chance after being played in by Oscar with 10 minutes remaining.
But he made amends moments later as after Dani had produced his only serious save of the day to turn Sola's header over.
From the resulting corner, Valladolid broke and Omar Ramos slipped in Ebert, whose delightful chip sealed victory for the visitors.
Defeat, allied to wins earlier in the day for Espanyol and Deportivo la Coruna, leave Osasuna four points from safety, while Valladolid continue their impressive start to life back in the La Liga as they move up into seventh.