The newcomers from Soria, who beat Barcelona 1-0 on the opening day of the season, took an early lead through Joan Carlos Moreno. Jose Barkero restored their advantage just after Guti had levelled for Real.
Gonzalo Higuain, Rafael van der Vaart on his league debut, and an own-goal from Domingo Cisma gave the home side what appeared to be a comfortable 4-2 halftime lead.
But Bernd Schuster’s side were the ones hanging on at the end after Moreno’s superb second-half free-kick had the visitors chasing an unlikely point in the closing stages.
Real, who lost 2-1 at Deportivo Coruna in their season-opener, were behind after only seven minutes when Moreno was gifted a free header at a corner.
Guti’s long-range effort deflected off a Numancia defender to level the scores at 1-1 in the 19th, Real’s 5000th goal in league competition.
But Numancia’s Barkero thumped a 20-metre drive into the top corner three minutes later, prompting another swift reply from the home side when Ruud Van Nistelrooy fed Higuain to level again at 2-2.
Van der Vaart’s snap shot beat Juan Pablo Colinas at his near post in the 34th and Cisma headed into his own net at a corner just before the break.
Numancia continued to press forward. Moreno curled a superb freekick in over the wall in the 57th and Real were against the ropes when Gorka Brit just failed to get a touch on a cross at the back post, in injury time.
“It was to be expected. These games after international weeks are always the hardest,” Schuster said.
“When we were 4-2 up we didn’t manage the game very well. We deserved to win by more but eased off too much in the second half.”
In the late game, Valencia twice come from behind to earn a 2-2 draw at Almeria, with goals from Alexis and David Villa cancelling out efforts from Pablo Piatti and Alvaro Negredo.
Earlier, Spain striker Luis Garcia snatched a late winner to give Espanyol a 1-0 away win over Recreativo Huelva and top place in La Liga.
Garcia completed a counter-attack by firing low into the far corner five minutes from time in a game with few chances for either side.
Espanyol have six points from two games, after beating Valladolid 1-0 at home in their season opener, and are two ahead of the pack with one match still to play this weekend.
Villarreal edged Deportivo Coruna 1-0 at home with a fine turn and shot from outside the area by Spain winger Santi Cazorla, in the first half.
Getafe joined Villarreal on four points after drawing 0-0 at home with Real Betis, missing out on the chance to join Espanyol at the top when Juan Albin crashed a late penalty against the crossbar.
Sevilla are second in the standings with four points on goals scored, after surviving a seven-goal thriller to beat promoted Sporting Gijon 4-3 at the Sanchez Pizjuan on Saturday.