Muldoon has recovered from a groin injury to be named at blindside flanker in a team that shows one enforced change to the side that beat Bourgoin 23-20 at the quarter-final stage.
Keith Matthews misses out due to an ankle injury, so his place at inside centre has gone to Aidan Wynne.
The 22-year-old Wynne is one of three members of the Grand Slam-winning Ireland Under-20 side from 2007 to feature in Connacht's starting line-up, with out-half Ian Keatley and prop Jamie Hagan being the others.
Keatley retains the number 10 jersey ahead of Miah Nikora, the late drop goal hero against Bourgoin, while in-form winger Fionn Carr will hope to add to his record of seven tries in seven European matches this season.
The Connacht bench includes England-capped prop Robbie Morris who had been a doubt with a calf injury.
Speaking ahead of Friday's game, Connacht coach Michael Bradley said: "Toulon embarked on a strategy which has got them to the top of the Top 14 and they have quality throughout their squad.
"They are a colourful side with big names and big stars with the likes of Jonny Wilkinson and Felipe Contepomi to pick and choose from.
"But they have to come to Galway and we have the X factor in terms of our ground. We have a home draw and, while they will bring the stars, we'll bring our support and we'll see who comes out on top.
"We went through the pool stages of the Amlin Challenge Cup unbeaten and we were able to carry that form through into the Bourgoin game.
"That sort of confidence has spilled over into our Magners League performances and we're having a good end to the season.
"The crowd were very important to us on the day against Bourgoin and obviously, in big cup matches, home advantage can count.
"The last time we were in a Challenge Cup semi-final we lost to Harlequins over two legs and they went on to win the tournament, so the fans are looking forward to the game against Toulon and it's going to be a massive game for us."
Admission to the ground is by ticket only and all tickets have been sold for this much-anticipatd game.
Car parking will be available at Moneenageisha Community College, at City Hall and city centre car parks, and also at Galwegians RFC on the Dublin Road. There will not be any public car parking available at the Sportsground.
Supporters holding tickets for the Main Stand side of the ground, and also the College Road Terrace, are asked to enter the ground at the main stadium turnstiles.
Supporters holding tickets for the Clubhouse Terrace and for the Bohermore Terrace are asked to enter the ground at the car park entrance to the ground.
For supporters who have purchased tickets online, Ticketmaster will have a collection box in the car park of the Huntsman Inn on College Road.
CONNACHT (v Toulon): Gavin Duffy; Troy Nathan, Niva Ta'auso, Aidan Wynne, Fionn Carr; Ian Keatley, Frank Murphy; Brett Wilkinson, Sean Cronin, Jamie Hagan, Michael Swift, Michael McCarthy, John Muldoon (capt), Johnny O'Connor, George Naoupu.
Replacements: Adrian Flavin, Ronan Loughney, Bernie Upton, Mike McComish, Conor O'Loughlin, Miah Nikora, Brian Tuohy, Robbie Morris.