Hernandez has recovered from an injury to his right hand to take his place in the squad, after missing the 63-9 loss to South Africa in August.
But injuries have forced prop Martin Scelzo, flanker Lucas Ostiglia and full-back Ignacio Corleto out of the selection.
Ignacio Fernandez Lobbe, Gonzalo Longo long-time captain Agustin Pichot have all retired, while Contepomi's twin brother Manuel is another notable absentee.
In all, there are eight players included from the Pumas team that started last year's 30-15 Rugby World Cup pool win over Ireland in Paris.
Rodrigo Roncero, Mario Ledesma, Patricio Albacete, Juan Martin Fernandez Lobbe, Juan Martin Hernandez, Horacio Agulla, Felipe Contepomi and Lucas Borges are all in line for another run-out against Ireland next month.
There are also four new caps in the 29-man panel - scrum half Agustin Figuerola, prop Juan Figallo, lock Mariano Galarza and prop Juan Pablo Orlandi.
Commenting on the squad selection, coach Phelan said: "After the defeat to South Africa, the idea is to have a fresh start. We must consider our position in the rankings ahead of the (2011) World Cup.
"This is a good chance to give the opportunity to young players we believe have the potential to progress.
"Juan Figallo was great in the Under-20 World Championship. He is a complete player.
"The same goes for (Juan Pablo) Orlandi, whose form for Argentina 'A' has been very good so it's good for them to join the tour.
"Mariano Galarza started at Universitario La Plata and we know him from his participation in the Buenos Aires regional team. He is very good technically.
'Agustin Figuerola and Nicolas Bruzzone are two young players who have been playing well. They are technically able so we want to profit from that."
With IRB World Ranking points on the line, Phelan said he is taking the Tests in Marseille (November 8), Turin (November 15) and Dublin (November 22) very seriously.
ARGENTINA European Tour Squad - Eusebio Guinazu (Agen), Horacio Agulla (Brive), Mario Ledesma (ASM Clermont Auvergne), Agustin Figuerola (CASI), Rafael Carballo (Castres Olympique), Martin Durand (Champagnat), Lucas Borges, Federico Martin Aramburu, Nicolas Vergallo (all Dax), Bernardo Stortoni (Glasgow Warriors), Gonzalo Tiesi (Harlequins), Santiago Fernandez (Hindu), Juan Figallo (Jockey Club Salta), Marcos Ayerza (Leicester Tigers), Felipe Contepomi (Leinster), Miguel Avramovic (Montauban), Rimas Alvarez (Perpignan), Alvaro Galindo (Racing Metro), Juan Pablo Orlandi (Rovigo), Juan Martin Fernandez Lobbe (Sale Sharks), Nicolas Bruzzone (SIC), Francisco Leonelli (Saracens), Juan Martin Hernandez, Juan Manuel Leguizamon, Rodrigo Roncero (all Stade Francais), Patricio Albacete, Alberto Vernet Basualdo (both Stade Toulousian), Esteban Lozada (Toulon), Mariano Galarza (Universitario La Plata).