The Pentagon announced the drawdown from Germany, its largest European base, on Friday, as a rift over the Iran war and tariff tensions place further strain on relations between the US and Europe.
As part of the US decision, a Biden-era plan to deploy a US battalion with long-range Tomahawk missiles to Germany has also been dropped.
That is a blow to Berlin, which had pushed for the move as a powerful deterrent against Russia.
Pistorius said the partial withdrawal was expected and would affect a US presence of almost 40,000 soldiers stationed in Germany.
"We Europeans must take on more responsibility for our own security," Pistorius said.
"Germany is on the right track" by expanding its armed forces, speeding up military procurement and building infrastructure."
Trump called for a reduced military presence in Germany as far back as his first term and has repeatedly urged Europe to take responsibility for its defence.
However, he stepped up the threat earlier this week after sparring with German Chancellor Friedrich Merz, who has questioned Washington's exit strategy in the Middle East.
The Pentagon said the troop withdrawal was expected to be completed over the next six to 12 months.
It did not say which bases would be affected, nor whether the troops would return to the US or be redeployed within Europe or elsewhere.
A NATO spokesperson said the alliance was working with the US to understand the details of the decision.
Polish Prime Minister Donald Tusk, whose country is seeking assurances of continued US support on NATO's eastern flank amid the ongoing Russia-Ukraine war, expressed concern about the latest setback to the alliance.
"The greatest threat to the transatlantic community (is) not its external enemies, but the ongoing disintegration of our alliance. We must all do what it takes to reverse this disastrous trend," Tusk wrote on X on Saturday.
The Pentagon's plans were the latest blow to Germany from Washington this weekend, after Trump said he would ratchet up tariffs on EU auto imports to 25 per cent, accusing the EU of not upholding a trade deal - in a move that threatens to cost the German economy billions.
A foreign policy official from Chancellor Merz's CDU party said the two announcements should be viewed in light of pressure on Trump both at home and abroad, amid weak opinion polling and pressure over unresolved conflicts in Ukraine, Venezuela and Iran.
"Against this backdrop, both the troop withdrawal and the trade policy seem less like the expression of a coherent strategy and more like a political reflex and a reaction born of frustration," Peter Beyer told Reuters.
NATO members have pledged to take on more responsibility for their own defence, but with tight budgets and vast gaps in military capability, it will take years for the region to meet its own security needs.
Germany wants to boost the number of active-duty Bundeswehr soldiers from 185,000 to 260,000.
The US military presence in Germany, which began as an occupation force after the Second World War, peaked during the 1960s when hundreds of thousands of American military personnel were stationed there to counter the Soviet Union during the Cold War.
The presence includes the giant Ramstein air base and Landstuhl hospital, both of which have been used by the US to support its war in Iran, as well as previous conflicts in Iraq and Afghanistan.
