Buckingham Palace announced the news on Thursday evening and play in the first round at Wentworth was immediately suspended with 30 players on the course.
The course and practice facilities were closed on Friday, but play restarted at 6.40am on Saturday with the tournament reduced to 54 holes.
A two-minute period of silence was scheduled for 9.50am.
“The decision to restart on Saturday has been taken in accordance with Official National Mourning guidance and in consultation with the Department for Digital, Culture, Media and Sport (DCMS),” the DP World Tour said in a statement.
“The Wentworth event will give players, caddies, staff, volunteers and spectators the opportunity to come together across the weekend, not only to express their condolences but also to celebrate the extraordinary life of Her Majesty.
“We join other sports in doing this, including the men’s Test match between England and South Africa at the Oval and the Women’s IT20 match between England and India in County Durham, Premiership rugby union, rugby league and the Great North Run in the north east of England.
“The Rolex Series event will now be contested over 54 holes with the intention to finish on Sunday as scheduled.
“It is not possible to play the full 72 holes and finish on Monday as we cannot guarantee the staff, facilities or security of the venue on Monday due to the ongoing plans for the state funeral.
“Across the weekend at Wentworth, black ribbons will be made available for people to wear and flags will continue to fly at half-mast.
“In addition, there will be a two-minute silence at 9.50am on Saturday morning across the venue to commemorate the life of Her Majesty Queen Elizabeth II, with the proclamation of King Charles III being shown on the television screens in the Championship Village from 10am.”
The second round started before the first had been completed, with England’s Andy Sullivan covering his first six holes in level par to remain tied for the lead on eight under with Tommy Fleetwood and Viktor Hovland.