I am using chromedriver with selenium and python.
I encountered same problem and following code worked for me-
driver.execute_script("window.confirm = function(msg) { return true; }")
prefs = {"protocol_handler.excluded_schemes":{"afp":True,"data":True,"disk":True,"disks":True,"file":True,"hcp":True,"intent":True, "itms-appss":True, "itms-apps":True,"itms":True,"market":True,"javascript":True,"mailto":True,"ms-help":True,"news":True,"nntp":True,"shell":True,"sip":True,"snews":False,"vbscript":True,"view-source":True,"vnd":{"ms":{"radio":True}}}}
chrome_options.add_experimental_option("prefs",prefs)
Let's say you want to suppress protocol handler popup for links starting with "sip://"
Just add an extra entry as "sip":True
in "protocol_handler.excluded_schemes"
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