Substitute Niclas Fullkrug (29) thundered in an 83rd minute goal to cancel out Spain's lead and earn the four-time world champions their first point from two matches following their shock opening loss to Japan.
That goal kept their hopes of advancing alive ahead of Thursday's final Group E match against Costa Rica which they must win.
"We knew what was at stake. Spain played good football but the teams were level and we had a huge chance in the end to win it but these things happen," Flick told reporters.
"Things come to you when you start winning. Maybe it is the spark we need."
Germany's Leroy Sane (26) missed a golden opportunity in the box minutes from the end but Flick said he was satisfied with his team's performance.
"The team fought hard and I am very satisfied with their mentality. These are the things we want and we know that we did take the first step.
"We want to have the conditions against Costa Rica to reach the knockout phase," said Flick.
Germany were teetering on the brink of elimination in the group stage for the second World Cup in a row but their draw combined with Japan's surprise loss to Costa Rica now moves the Germans into positive territory.
"Costa Rica showed good mentality to come back from a 7-0 loss to Spain (and beat Japan)," Flick said.
"Football is like that. Sometimes it's not those with the most chances that win. We experienced that against Japan."
Germany are on one point with Costa Rica and Japan on three. Spain, who next play the Japanese, are on four.
Flick said he would not rush to focus on Costa Rica, knowing that his players needing to process Sunday's game first.
"It is still too far away to think about Costa Rica. We have to let this game sink in and generate self confidence."
Asked whether he had watched Costa Rica's win earlier, Flick said he had not but heard "a small celebration" from his team following the result.
