Wieczorek-Zeul said they had discussed Tibet and its ties with China as well as human rights, poverty and globalization during their 45-minute meeting in Berlin's posh Hotel Adlon.
"I stressed how important peaceful dialogue with China can be," she told reporters, saying the meeting had been fruitful and reiterating Berlin's demands for direct talks between the Tibetan representatives and Beijing.
It was the highest-level political meeting yet of the Dalai Lama's latest tour of Western nations that is likely to keep the spotlight on Tibet after deadly anti-Chinese unrest rocked the regional capital Lhasa in March. Monday is his last day in Germany.
China this month resumed talks with Tibetan envoys in a move seen as a response to condemnation of its military crackdown on the protests - which caused international controversy in the runup to the Beijing Olympic Games.
German Chancellor Angela Merkel, who infuriated Beijing last year by meeting the Dalai Lama and backing his quest for cultural autonomy for Tibet, on Monday welcomed the Beijing-Tibet talks.
"The Chancellor expressly welcomes the resumption of dialogue," government spokesman Thomas Steg said, adding that Berlin trusted the Dalai Lama's meeting with a German minister would not jeopardize the process.
"We do not believe that today's meeting will have a negative impact on the dialogue forming between China and the Dalai Lama's representatives on developments in Tibet and perhaps also in neighbouring regions."
But the meeting unleashed a storm of disagreement within Wieczorek-Zeul's Social Democratic Party (SPD), with Foreign Minister Frank-Walter Steinmeier reported to be furious that the development minister failed to inform colleagues of her plans.
Steinmeier, also a Social Democrat, opposed the meeting eight months ago between the Tibetan spiritual leader and Merkel, whose Christian Democrats (CDU) are the senior partner in Berlin's ruling coalition with the SPD.
"None of us knew that Heidemarie Wieczorek-Zeul wanted to meet the Dalai Lama," SPD chairman Kurt Beck said while in the northern German city of Lübeck over the weekend, according to a report in German newspaper Welt am Sonntag.
And by the time he found out about the planned meeting, "it was too late to call the shit off," Beck is reported to have said.
SPD deputy parliamentary whip Walter Kolbow said on Monday in German television broadcaster ZDF that while Wieczorek-Zeul had the right to meet with the Dalai Lama, she was making Steinmeier's job more difficult.
Merkel will not meet the Dalai Lama during this visit because she is in Latin America, but her outspoken support for his quest for cultural autonomy for Tibet - and suspicions that she encouraged Wieczorek-Zeul to receive him - has caused further strife in her fraught ruling coalition.
Wieczorek-Zeul referred to the row on Monday, telling reporters that she had discussed the SPD's concerns with Beck and defending herself against the criticism from within her party.
"I don't think that's fair to the people in the affected region or to the character of the Dalai Lama," she said. "That's why I intentionally decided not to take this sort of party politics into consideration."
The Chinese embassy has also objected to the exiled leader's talks with Wieczorek-Zeul and accused him of "playing politics" in the run-up to the Beijing Olympic Games in August.
"We object to a member of the German government receiving the Dalai Lama and to Germany allowing him to carry out this visit," Junhui Zhang from the Chinese embassy in Berlin told the press last week.
The 1989 Nobel peace laureate began his five-nation tour in Frankfurt last week with an attack on China's military crackdown on Tibetan protestors, accusing Beijing of "suppression."
Flag-waving supporters met him on Monday in Berlin, but a speech at the Brandenburg Gate later in the day was expected to draw Chinese protestors.
After Germany, the Dalai Lama is to head to Britain, Australia, the United States and France in a three-month tour ending in mid-August just before the end of the Beijing Games.