It was their fifth loss in a row and saw them eliminated from the United Rugby Championship quarter-finals.
Glasgow also reached the last eight of the European Challenge Cup but were beaten by Lyon.
The club began the season well and were in the top four of the URC for much of the campaign but ended up finishing eighth after a dispiriting loss to Edinburgh at Murrayfield which saw them lose the 1872 Cup and miss out on a place in next season’s Heineken Champions Cup.
Glasgow will now begin the process of looking for a new head coach.
Wilson, who was employed previously as Scotland’s forwards coach and had a year left on his Warriors contract, took over from Dave Rennie in summer 2020 and had to contend with the Covid disruptions in his first season in charge. He managed to steer Glasgow into a position where they qualified for the 2021-22 Champions Cup and the club also won the 1872 Cup for the first time in four years.
But supporters began to express their disgruntlement during his second season in charge, culminating in the decision to dispense with his services.
“The recent run of results has not been acceptable and has had a significant impact on everyone connected to the club,” said Al Kellock, the Glasgow Warriors managing director.
“We are a proud organisation and want to be competitive week in, week out and we felt therefore a change of head coach was the right step to take.
“It is never pleasant to have to make changes to our team, but we needed to act. I’ve enjoyed working closely with Danny and know he has given a huge amount to Glasgow over the past two seasons and for that I’d like to thank him and wish him well.”
Mark Dodson, the Scottish Rugby chief executive, said: “I’d like to thank Danny for his contribution to rugby in Scotland over the past four years.
“He faced a challenging period taking on the Glasgow role mid-pandemic and while there have been several high points, ultimately recent results have not been consistent enough and given the importance of our two professional teams we needed to address that in a timely manner.
“I have a lot of respect for Danny and the professional way he conducts himself and wish him well in the future.”
In announcing the decision, Glasgow Warriors said in a statement: “Scottish Rugby and Glasgow Warriors can confirm that Head Coach Danny Wilson has been stood down from his role with immediate effect.
“The decision was taken by the club and Scottish Rugby following a meeting with Wilson earlier today (Monday 6 June).
“Scottish Rugby would like to thank Danny for his contribution over the past four years, firstly with the men’s national team and subsequently with Glasgow Warriors.
“The squad will break for the close season at the end of this week and the club will now begin a recruitment process for a new Head Coach.”