Merkel, like Greece's hard-left Prime Minister Alexis Tsipras, faced rebels in her own party ranks, but still won broad approval from the chamber where her "grand coalition" commands an overwhelming majority.
The measure to seek a new 86-billion-euro (USD 94 billion) rescue package sailed through the Bundestag by 439 to 119 votes with 40 abstentions.
Addressing the chamber before the vote, Merkel had argued that "we would be grossly negligent, indeed acting irresponsibly if we did not at least try this path".
The chancellor said there was "no doubt that the agreement of Monday morning was hard" but urged lawmakers to back the deal, calling it "a last try".
Also Read
She said if a compromise over Greece had not been reached, it would have meant "watching on as the country virtually bleeds out, people no longer getting their money, where chaos and violence could be the result".
That was why, she said, "we are making a last try in tough, tenacious discussions" to seal a third aid package, "despite all the setbacks of the past six months and despite all legitimate scepticism".
The German 'Yes' vote came a day after European Central Bank chief Mario Draghi boosted a vital cash lifeline to Greece's struggling banks that will allow them to open their doors for the first time in almost three weeks on Monday.
The about-face sparked violent street protests and speculation of early elections in Greece, where the hard-left Syriza party came to power in January polls.