Valencia thought he had given the South Americans a third-minute lead, heading past Maroons goalkeeper Saad Al-Sheeb, but video review showed there was offsides in the build-up play.
In the 16th minute, the former West Ham striker did open the scoring as Al-Sheeb brought him down in the box and Valencia sent him the wrong way.
The lead was doubled shortly after the half-hour mark as another header by Valencia from the left gave Ecuador a 2-0 advantage and they would never be seriously threatened.
Story of the match
Shortly after the opening whistle and for them, a moment 12 years in the making, Qatar was off and running, sending in a dangerous long ball that Ecuador were able to deal with.
It wouldn't take long for the tournament's first moment of controversy. Following a La Tri free-kick, Al-Sheeb raced off his line, but Pervis Estupinan volleyed the ball across goal with Valencia on hand to head home.
However, referee Daniele Orsato checked with VAR, now including semi-automated offside technology, which determined Michael Estrada's foot was in an offsides position in the build-up, nullifying the goal.
Ten minutes later, Ecuador would take the lead. Valencia was played through by the Maroons defense and after rounding Al-Sheeb, he was fouled in the box.
The Fenerbache frontman calmly stepped up to the spot and rolled home low and to the right, sending Al-Sheeb the wrong way.
On 31 minutes, the South Americans were two goals to the good, Qatar giving away possession and Angelo Preciado crossed into the center of the box where Valencia was waiting to head past a helpless Al-Sheeb.
A minute after the goal, the tournament hosts recorded their first shot of the match, defender Abdelkarim Hassan strode forward and had a go from distance, but was nowhere close to hitting the target.
The Maroons' first threat into the final third of Ecuador should have resulted in their first-ever World Cup goal, Hassan Al-Haydos getting free down the right and his cross found an unmarked Almoez Ali, who somehow glanced his header wide from close range.
Al-Sheeb was tested ten minutes into the second half, Romario Ibarra sizzling a shot that stung the goalkeeper's palms from 18 yards away.
In the 61st minute, the Maroons had another opportunity, right-back Pedro Miguel flashing in the center to meet a cross at the top of the box, winning the header, but sending it wide.
Akram Afif, the hosts' other star forward, tried his luck from long range with 15 minutes to go, but could only blaze it well over the bar.
Valencia, who was shaken up late in the first half, came off shortly after Afif's miss and was replaced by Jose Cifuentes.
Muhammad Muntari nearly made it a grandstand finish, attempting a hopeful volley from 18 yards, his strike dipping over La Tri goalkeeper Hector Galindez and under the crossbar, but it went just over.
Player of the match: Enner Valencia
Became Ecuador's all-time leading World Cup scorer with his fourth and fifth goals and should have had a hat-trick. Took his chances well and proved to be a constant threat whenever he was in a position to attack.