The competition holders won 19-14 at Bath but Wasps got a bonus-point in defeating Leinster 51-10 to sneak ahead of Toulon atop the standings.
Both sides went through to the quarter-finals but Toulon now face an away tie against one of the other group winners.
“It’s a huge satisfaction. OK, we finished second in the group despite having won five matches compared to Wasps’ only winning four, but those are the rules regarding the bonus points,” said Toulon manager Bernard Laporte. “Anyway, Wasps deserved to qualify. It was up to us to deny them a (losing) bonus point at Mayol and even more so (a try bonus) at their place.
“But I’m very proud of our team because we’re missing important players but that didn’t stop us progressing.”
Bath fell behind to two James O’Connor penalties, before George Ford’s three-pointer got the hosts going.
Toulon extended their lead when England exile Steffon Armitage powered over.
Anthony Watson hit back when he touched down after good work from Horacio Agulla and Kyle Eastmond. Ford missed the conversion before landing a penalty to give Bath a 14-11 lead.
But flanker David Denton gave the ball away to South Africa wing Bryan Habana and he sprinted over to score an easy try for Toulon.
O’Connor missed the conversion but his third penalty sealed the deal for the French side.
In Coventry, Leinster struck first with a second minute Zane Kirchner try and Eoin Reddan’s score on the half hour brought the Irish province back to 12-10.
But after that, Wasps started to pull away. Jimmy Gopperth, who finished with 19 points, notched their first try before Joe Launchbury, Elliot Daly, Frank Halai, Charles Piutau and Ashley Johnson all scored as Wasps ran amok.
Meanwhile, Ulster kept their quarter-final hopes alive with an eight-try, bonus-point 56-3 victory over Oyonnax.
Tries from Rob Herring, Darren Cave, Rory Scholes, Sean Reidy, Craig Gilroy, Robbie Diack, Ian Humphreys and Jared Payne meant Ulster finished the group stages on 18 points, well behind runaway pool A winners Saracens who ended with a perfect six wins from six
after winning 28-17 at Toulouse.
In Pool 3, Northampton face an anxious wait after a 22-10 win at Scarlets confirmed a runners-up spot in Pool 3.
Harry Mallinder, George Pisi, Sam Dickinson and George North scored to helps Saints claim a bonus point, but results today will dictate whether they go through as one of three best runners-up. Racing 92 won the section despite a 22-5 loss at Glasgow.
