Howley, who is serving as caretaker head coach in the absence of RBS 6 Nations winner Warren Gatland, saw his side throw away a 12-6 lead as the Pumas came storming back in the final third of the game.
The boot of full-back Leigh Halfpenny looked to be guiding Wales to a hard-fought if uninspiring victory as he slotted four penalties.
But Argentina are made of stern stuff these days after a debut season in the Rugby Championship alongside Southern Hemisphere heavyweights the All Blacks, South Africa and Australia.
And second-half tries from Juan Imhoff and Gonzalo Camacho left the reigning RBS 6 Nations champions staring down the barrel and the boot of fly-half Nicolas Sanchez did the rest to leave Howley fuming.
“I am disappointed, frustrated and annoyed because we know we are a better side than that,” said Howley, who now faces an uphill battle if Wales are to grab fourth-place in the IRB rankings from England before the 2015 World Cup draw is made.
“We talked about it being an arm wrestle for 50 minutes and we were 12-6 ahead but we looked one-paced.
“When you play Argentina, tempo, pace and intensity are important but there is no doubt their experience and exposure to the Rugby Championship has taken that Argentina side to another level.
“They played the All Blacks, South Africa and Australia over a six-week period and they have certainly learned from that and we were exposed to it today and we very much came second.”
And things go from bad to worse for the Welsh, who face Samoa next at the Millennium Stadium, as stalwarts Jamie Roberts and Alun Wyn Jones both limped off with serious looking injuries.
Both of them would be big losses for the rest of the autumn series and Howley admits the outlook does not look great.
“Jamie has a bump on the head, it’s a mild concussion to say the least," he added.
"Alun Wyn has done his AC (joint) so we will have to wait on the medical opinion for that but it does not look good at this time and it will test our strength in depth as these next three games are very important.”