The 19-year-old Australian attacker was substituted off at halftime of the Hornets' 2-1 English Championship win at Vicarage Road against West Bromwich Albion by new manager Javi Gracia.
Gracia, whose first stint as Hornets manager ended in September 2019, was rehired last week to replace Paulo Pezzolano.
The Uruguayan was sacked after just 10 games in charge and a sideline bust-up with fan-favourite Irankunda, who has scored twice in 11 outings since joining from Swiss club Grasshopper.
Whether travelling to and from North America, where he scored the winner against Canada and played the final 30 minutes off the bench in the loss to the United States, was the major reason for being given a rest after the break is unclear.
But the former Adelaide United wonderkid looked tired on Tuesday night, made several unforced errors and poor decisions in the first half in which his side went behind before scoring twice.
Irankunda's replacement, Mali international Mamadou Doumbia, had perhaps his best half in a yellow shirt.
"In this moment I thought it was the best option to be more aggressive, to press higher and to control the game with two players upfront," Gracia said.
"I think it was a good solution in that moment."
Albion would have gone up to third had they won but ended the day in 10th spot, two points and two places above Watford.
There are also concerns too for Irankunda's compatriots Riley McGree, Sammy Silvera and Cam Burgess.
Middlesbrough's attacking midfielders McGree and Silvera were unused substitutes in the 1-0 victory over bottom-placed Sheffield Wednesday, which consolidated second spot, one point behind leaders Coventry City.
For the second game running since coming back from his latest injury, McGree was selected but not called upon by manager Rob Edwards, who has spoken highly of the versatile 26-year-old.
"He's looked great in training and we know the qualities he's got," Edwards said.
"He's certainly someone who is really intelligent and so good technically, so he can fit for us in different positions.
"He gives us a really nice problem when he's at full tilt."
Burgess, meantime, played a full game but his Swansea City side were beaten 1-0 at home by Queens Park Rangers.
QPR have lost just one of their last eight matches and sit eighth, while the Swans drop to 16th.
Elsewhere, another Welsh club in Wrexham recorded their first home league victory since gaining promotion.
Nathan Broadhead scored a first-half winner as the hosts beat Oxford United 1-0 to go 15th and leave the U's one point and two places above the drop zone.
With PA.
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