Just two weeks after the European Commission failed to secure a majority, an intervention on Monday meant 18 of 28 EU states were now in favour and glyphosate was granted a new five-year licence.
Glyphosate - introduced under the name Roundup by USA agriculture giant Monsanto in 1974 - previously had a 15-year licence but it expired in June 2016.
European Union health and food safety commissioner Vytenis Andriukaitis said: "When we all want to, we are able to share and accept our collective responsibility in decision-making".
"Habemus glyphosate" say Brussels as Monday's appeal committee meeting, maybe the last chance for the bloc to "save" the "probably carcinogenic" substance, one of the most widely used herbicides.
While his position mirrors that of most British farmers, it contrasts with the concerns of environmentalists and other campaigners anxious by the chemical's alleged health risks.
"Today's approval, even if only for five years, is a missed opportunity to get rid of this risky weedkiller and start to get farmers off the chemical treadmill".
"Anyone who is interested in developing trust between two parties can not behave that way", she said. Under EU rules, 16 favorable votes are needed as a "qualified majority" for renewal before authorization expires on December 15.
However, German Environment Minister Barbara Hendricks, of the Social Democrats who had initially refused to consider renewing their coalition with Merkel, said Agricultural Minister Christian Schmidt of the Merkel-allied CSU party had gone against her orders. The European Chemical Agency said in March this year, however, there was no evidence linking it to cancer in humans.