Groenewegen beat Dan McLay (Arkea-Samsic) and Davide Ballerini (QuickStep-AlphaVinyl) in the dash to the line after Aussie Caleb Ewan (Lotto Soudal) suffered a late puncture and was unable to contest the sprint, giving up his red points jersey in the process.
Van Gils won the overall classification by 36 seconds ahead of Santiago Buitrago (Bahrain Victorious) and 48 seconds ahead of Rui Costa (UAE Team Emirates).
"The boys did a really good job," Groenewegen said after the stage.
"They’ve learned really soon and have tried to do things as good as possible and now we have two victories. I think it’s two out of three, so it’s really nice.
"We lost each other a little bit, but in the final we found each other and Luka (Mezgec) and me came together on the roundabout. It was a really good job from the team, they put me in a really good position in the end, I think maybe 200 metres before the finish, Luka put me in position, he made a really good move to go to the right and I had some space to go very well and very free, so it was a good sprint.
It’s a really good start of the season, I was a little bit nervous before the start of the season in a new team, but everyone has learned so fast and everybody did a really good job today."
With wind much less prevalent after yesterday's echelon-filled Stage 4, a four-man breakaway dominated much of the early action, as Jannik Steimle (QuickStep Alpha-Vinyl), Polychronis Tzortzakis (Kuwait Pro Cycling) and Anthon Charmig and Martin Urianstad (both Uno-X) gapped the peloton by as much as 2 minutes as the race approached the finishing circuit of AlUla Old Town.
Tzortzakis was the first to bow out as the gap got down to under a minute and Charmig followed shortly after, making Urianstad and Steimle the sole leaders before Steimle launched a big attack out of a left-hand bend to go solo inside the last 20 kilometres.
His hopes of a win were dashed as the peloton closed him down with 10 kilometres to go and the lead-out trains began to form for the oncoming bunch sprint, with BikeExchange-Jayco, BORA-Hansgrohe, Lotto Soudal and Bahrain Victorious taking turns to pull at the front.
Tim Declerq (QuickStep Alpha-Vinyl) launched an unlikely attack which was quickly roamed in as the group stayed tight inside the last five kilometres, and just when it was looking interesting disaster struck for Ewan.
The Stage 1 winner dropped back from the group within the last three kilometres with an apparent tire puncture, bringing to an end his hopes of contesting both the sprint and the points classification after wearing the red jersey coming into the day.
BORA-Hansgrohe led the pack into the final kilometre, launching an early leadout for sprinter Danny van Poppel with Luka Mezgec (Bike-Exchange Jayco) and Groenewegen close behind as they rounded the turn into the finish.
Groenewegen latched on to van Poppel's wheel as the Dutchman kicked inside the final 300 metres before he timed his own acceleration to perfection to beat out the rest of the stage hopefuls and take the victory.
