Pietersen, England's captain from 2008 to 2009, insisted Monday the fundamental issue was the ability of the squad available to Root, who has skippered the Test side on a record 64 occasions, rather than his much-criticised tactics in the field.
"As a captain you are only as good as your players," Pietersen told Talk Sport radio.
"Forget Joe Root, it is about the players. Who is going to do a better job with the calibre of player that is playing Test cricket for England? It is not Joe Root's fault. Who are you going to pick?"
Pietersen, 41, added: "When Jack Leach and Ben Stokes put that partnership together at Headingley (in the Ashes) three years ago, Stokes played the innings of his life -- I said then Leach is not good enough.
"He's not a good enough spinner. And who is second in line, Dom Bess? Are you joking?
"Don't point fingers at Root, understand the set-up. The set-up stinks."
Ben Stokes, currently England's vice-captain and a close friend of Root, would appear to be the obvious successor as skipper.
But the 41-year-old Pietersen, a gifted batsman who scored 23 hundreds in 104 Tests, insisted a change of captain would mean little if the team kept suffering top-order collapses.
"How is he (Stokes) going to do any better than Joe Root?... How are you going to get these guys scoring runs against the best bowlers in the world?
"Have you see what's coming? New Zealand, India, South Africa.
"How are you going to get these guys scoring 200s? Number one, two, three, four and five, how are you going to get them scoring 200s when they can't bat?"
Boycott, another former captain said England, now bottom of the World Test Championship table, were "going nowhere".
"They need a rocket up the backside from a new head coach with some fresh ideas," Boycott wrote in his Daily Telegraph column.
"Doing nothing is not an option. Nothing is working," added Boycott, one of England's all-time great opening batsmen, who did not spare Root, a fellow Yorkshireman, as he called for a "shake-up" in personnel.
"The captain, Joe Root, is incapable of lifting these players," Boycott insisted.
"England are not losing because they are unlucky. They lose because they just aren't good enough."