Tour rookie Van Avermaet was overjoyed with his stage win.
"It's my first season and already my first success amid the professionals," he said. "I know I'm quick - that was my strength in the amateur ranks - but against my new breakaway companions, I really lacked any markers and I had no idea of my level compared to them. Now I've got them," he joked.
The stage was marked by rain and strong crosswinds but several riders attacked from the start.
A group of 10 riders hit the front of the race at 40km and after an hour they were more than two minutes ahead of the peloton.
The first sprint at 55km was won by Van Avermaet and at that stage they had opened their lead to nearly four minutes. But the main bunch pulled that back to just 45 seconds after Boonen suffered a puncture.
It took Boonen 20km to get back into the peloton but his return calmed things down and the breakaway group opened up another big lead.
The leaders stayed together until 2km from the finish when Cretskens tried to twice to sprint for the finish but Van Avermaet powered past him with 50m remaining.
At the finish, Cretskens realised that he was just one day away from his first stage race win as a professional.
"Yeah for me it's also a surprise," he said.
"At the start, we talked to each other in the team. It was very important if break went that we had someone in it. We did a good job at the beginning. Everybody tried to be in the break and it was me."
Friday's sixth and final stage sees the riders tackle a 134km course between the Sealine Beach Resort and Doha.