The Barcelona B loanee decided the game by netting the only goal shortly before half-time, but Valladolid were incensed it was allowed to stand.
Despite the controversial manner of the goal, the hosts just about deserved the win, creating the better of the chances.
The visitors' frustration grew further when Patrick Ebert was sent off late in the second half for receiving two bookings.
Almeria were looking to build on their first win of the season, which came away to Valencia during the week.
Valladolid, meanwhile, had fought back from a two-goal deficit to draw with Real Sociedad.
The first half was end to end, even though neither side created many clear cut chances. Soriano had the ball in the net for the hosts just after the half hour mark, but it was ruled out for a foul by Rodri on Valladolid goalkeeper Diego Marino.
The visitors' stopper had almost gifted Almeria a goal moments earlier when he misplaced a pass which landed at the feet of Aleix Vidal. The midfielder squared to Fernando Soriano, but he panicked and the danger was cleared.
The controversial goal arrived eight minutes before the break. Suso put a cross into the six-yard box and Rodri slid in to meet it, converting the ball into the net with his hand.
The goal was fiercely contested by the Valladolid players and Rodri himself hesitated before celebrating, but referee Cesar Muniz Fernandez, who was suspended from duty last month after awarding a questionable penalty to Real Madrid at Elche, allowed it to stand.
Almeria grew in confidence after the break and should have doubled their lead.
Marino was on hand to deny Verza and Ramon Azeez on separate occasions, while Suso and Rodri got in each others way with the goal gaping after Esteban had parried a shot from Vidal.
Ebert was then sent off after receiving his second yellow card, for an elbow on Azeez.
In the dying moments Marino tipped a shot from Azeez over the bar but when the final whistle blew, Valladolid players surrounded Muniz Fernandez again, adamant they had been robbed of the points by an inexplicable decision.