Jose Antonio Camacho's side took a shock lead at the Bernabeu on 20 minutes when Iranian midfielder Javad Nekounam outleapt Fabio Cannavaro to nod Jaroslav Plasil's cross past Iker Casillas.
An error by goalkeeper Roberto Fernandez gifted Real an equaliser just after the break, a long-range Sergio Ramos shot spooning into the net off his hands, and Gonzalo Higuain netted shortly after, tapping home Arjen Robben's low cross.
In-form Robben made sure of the points in added time, cutting in from the right and driving the ball past Fernandez.
It was the fourth consecutive league victory for the champions and ends a turbulent week away from the pitch with the resignation on Friday of President Ramon Calderon.
The match ended in controversy after Osasuna midfielder Juanfran was shown a second yellow card for diving when he appeared to have been fouled in the area by Pepe.
His earlier caution had also come after a penalty claim when Fernando Gago looked to have felled the former Real player on the edge of the box.
"I come back here after four years to try to play well for my team and I get sent off because of mistakes by the referee," Juanfran said in a radio interview. "It hurts a lot."
RECORD POINTS
Real's win follows Barcelona's 5-0 thrashing of Deportivo Coruna at the Nou Camp on Saturday.
The Catalans have amassed a record number of points for the first half of a season, with 50 from 19 matches, eclipsing the previous best of 47 set by Real Madrid last term.
"Barcelona are playing very well and producing some magnificent football," Real coach Juande Ramos said at a news conference.
"Madrid is not playing as well but has been achieving good results for the last month and that creates confidence and allows you to play much better."
In other matches on Sunday, Atletico Madrid ended a run of four straight losses but could only manage an ugly 1-1 draw at Almeria and relinquished fifth spot to Villarreal, who beat struggling Real Mallorca 2-0.
Fernando Llorente's penalty in added time snatched a 3-2 win for Athletic Bilbao against fourth-placed Valencia as the Basque side twice came from behind in an ill-tempered clash at the San Mames. Malaga thumped Espanyol 4-0 to climb to seventh ahead of Deportivo in eighth and Athletic in ninth.
