He told MSPs of passengers' frustrations at hearing their stop would be skipped after they had started their journey.
Mr Yousaf was responding to Midlothian South, Tweeddale and Lauderdale SNP MSP Christine Grahame, who highlighted Scotland on Sunday's revelation that 20 trains a day skipped stops.
He said: "In some instances, the ScotRail Alliance feel that skip stopping has to take place...in order for the entire network not to be out of kilter.
"What is clearly unacceptable, and what happens far too often, is the communication round that.
"People are already on the train and then their stop is missed out and skipped.
"If people knew in advance that the train was not going to stop then perhaps they could plan their journeys ahead.
"There is clearly a failure in communication."
He said stop skipping was "undeniably and understandably unpopular.
"It an area my officials at Transport Scotland will continue to monitor and challenge ScotRail on to ensure that practice is minimised.
The minister said a review to improve ScotRail's under-par performance was looking at how to reduce stop skipping.
Mr Yousaf told MSPs last week that 0.78 of ScotRail's 2,500 trains a day, or some 20 services, skipped stops in 2017.
This compares to 0.6 per cent, or 15, in 2016-17.
Scottish Greens transport spokesman John Finnie said: “Stop skipping is a most inconvenient practice which can leave passengers stranded miles away from their intended destination.
"I was pleased the transport minister acknowledged the current situation is not good enough and recognised that improvement must be made in communication with passengers.
"It is also vital the minister conducts an equality impact assessment to ascertain the unnecessary inconvenience this practice causes to those with mobility issues.The ScotRail Alliance said all its information outlets, such as platform boards and automated announcements, were updated as alterations were made to a service.
A spokesperson said: “We understand how frustrating it can be for customers when their journey is disrupted.
"We only miss out scheduled stops at times of major disruption, to prevent further delays across the network.
“We work hard to provide customers with as much notice as possible about any potential disruption to their service by updating our app, website and social media feeds at the earliest opportunity.
“We always look at how we can communicate better with our customers when there is disruption, and this is something we keep under constant review.”