First, I want to clarify that the USSR and Germany were supporting opposite sides in the Spanish Civil War - the former supported the Republicans while the latter supported the Nationalists. Secondly, they were never really allies in the strict sense of the word. There was a non-aggression pact (the Molotov-Ribbentrop pact), a divvying up of spheres of influence, and commercial ties. But that was it. There was some discussion about the USSR joining the Tripartite Pact (with Italy and Japan) that would have created an actual alliance but that went nowhere.

To get back to your actual question, well, initially the USSR was quite anti-German. During the late 1930s, Stalin wanted to make a new alliance with France and United Kingdom to contain Germany. The USSR entered an agreement with France to mutually defend Czechoslovakia if it were attacked by Germany. In 1939, France and Britain also sent their representatives to Moscow to hammer out a comprehensive agreement that would involve all three parties.

However it soon became obvious that the western allies (particularly Britain) were not really interested. The Munich Agreement, the policy of appeasement, and other foot-dragging showed that the allies were not serious about being allies with the USSR (perhaps for understandable reasons given Soviet ideology and the repressive regime). The Soviet Union was thus left politically and militarily isolated. At that point, Stalin decided to change course toward closer ties with Germany. This was done to make sure that the USSR would be dragged into the war, at least initially. The Red Army wasn't ready for a major war, and Stalin wanted to buy time. Taking a chunk of Poland also moved the Soviet border westward by about 200 miles, farther away from major Soviet cities and industrial centers.

Germany, for its part, didn't want a war with the USSR at that point in time, and also needed Soviet oil and natural resources. But both Germany and the USSR understood that their arrangements were just temporary.