The counter-protesters, carrying a range of flags and placards, many defending diversity and freedom of the press, marched in the northern city.
Police put the total turnout for two separate counter-demonstrations at 7,000. They said around 120 members of the far-right National Democratic Party (NPD) turned out for their protest.
Earlier in the week, police had tried to ban the NPD demonstration, arguing it posed a danger to public safety, but on Friday a court ruled that it could go ahead.
The NPD called their demonstration to denounce journalists — a number of whom they named — who have investigated the far-right in Germany.
German Foreign Minister Heiko Maas tweeted: “We were able to see in Hanover what is true for all of Germany: the neo-nazis and fear-mongers who stir up hate against journalists are a minority.”
One journalist the NPD singled out was Julian Feldmann, who made a programme for German state television about suspected Nazi war criminal Karl Münter, implicated in a 1944 massacre of 86 people in Ascq, northern France.
In a television interview, former SS soldier Münter blamed the victims of the massacre and also made negationist remarks about the Holocaust. While awaiting trial on charges of incitement and disparaging the memory of Nazi victims, Münter died at the age of 96 in September.
Founded in 1964, the NPD has around 6,000 members.
In January 2017, the constitutional court, the highest jurisdiction in Germany, rejected moves to ban the party — the second time it has blocked such a move in 15 years.