Pulling no punches, Howley declared: "I am disappointed, frustrated and annoyed because we know we are a better side than that. 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."
The Six Nations champions led 9-6 at the break thanks to three Leigh Halfpenny penalties, with Felipe Contepomi slotting a penalty and Nicolas Sanchez landing a drop goal for the Pumas. Halfpenny extended Wales' lead with a fourth penalty early in the second half, but a penalty and drop goal from Sanchez, plus converted tries for wings Juan Imhoff and Gonzalo Camacho saw the visitors secure their second win over Wales in Cardiff, 11 years to the day after their first.
The defeat puts a major dent in Wales' hopes of securing a top-four place in the world rankings ahead of next month's 2015 World Cup draw, but they can have no complaints after being exposed by Argentina.
There looks set to be further bad news after a clearly concussed Jamie Roberts was helped off after a clash of heads with Gonzalo Tiesi, while lock Alun Wyn Jones was withdrawn with a shoulder problem just before the break, putting their involvement in the rest of the autumn series in doubt.
Assistant coach Shaun Edwards was as scathing as Howley in his assessment of the performance, and felt Wales had badly missed the injured trio of centre Jonathan Davies, prop Adam Jones and flanker Dan Lydiate, as well as Roberts after he went off.
He said: "I definitely thought the impact from the Argentina bench was better than ours. We went into the game with certain personnel missing and it showed badly in the last half hour."
Argentina coach Santiago Phelan agreed with Howley's view that his side's experience in the Rugby Championship played a big part in their victory, which tees them up perfectly for their remaining tour fixtures against France and Ireland.
"We are very happy with our performance today," he said. "The team took the initiative in the first 20 minutes and played very well in the second half, moving the ball and keeping possession.
"The intensity of the game was very high, but the players have had a good experience playing in the Rugby Championship and have learned to play at this intensity.
"Today was a good step forward for our team."