Thompson died on Wednesday after a long battle with cancer.
SPL executive chairman Lex Gold described the death of Thompson as "a great loss to our game."
Gold said: "At this time our thoughts are with those close to Eddie. We send our condolences to his wife Cath, children Stephen and Justine, their families and all at Dundee United.
"Eddie's incredible enthusiasm for Dundee United, the SPL and football in general made him an inspiration to many. He is a great loss to our game.
"On a personal level, I am pleased to have been able to work with Eddie and I will miss his support, encouragement and insight."
The SPL also confirmed there would be one minute of applause for Thompson before all other top-flight games in Scotland this weekend.