The Highlanders deservedly struck four minutes from the break and held fast during a more even second half to claim the 1-0 win that ensured they kept pace with Dundee United in fourth place above them on goal difference.
Caley Thistle have reached the League Cup final and the quarter-finals of the Scottish Cup in recent weeks but have seen their Premiership campaign stutter, with just two victories arriving since Hughes took over from predecessor Terry Butcher in December.
However, guided on the pitch by the stoical skipper Richie Foran, Inverness were well worthy of their three points against a lacklustre St Johnstone side who saw defender Frazer Wright taken off on a stretcher eight minutes from the break.
Inverness could, and perhaps should, have been ahead after just a minute of the match.
A cross from deep from Josh Meekings found eventual match-winner Warren lurking on the edge of the six-yard box but the big centre-half could not direct his diving header on target.
Five minutes later, the Highlanders threatened again.
This time, a Billy McKay shot was beaten away by Alan Mannus and Greg Tansey's drive from the resulting play slipped just wide of the upright.
After a period of respite for St Johnstone, Caley Thistle went close five minutes from the break.
Excellent build-up play involving Aaron Doran brought Marley Watkins into play on the right side of the box and his first-time ball back in for McKay brought Mannus out to dive bravely at the striker's feet.
Hughes' men were not to be kept at bay, however, and finally took the lead in the 42nd minute.
Watkins laid the ball back for David Raven to swing in a high cross and when Foran nodded the ball down and back up into the air it was Warren who reacted strongest to power a header into the top corner from six yards out.
Where Caley Thistle were full of vigour and energy, St Johnstone were flat.
The home side were always a threat on the break in the opening period but attacks were all too sporadic as the visitors bossed the half throughout.
Nigel Hasselbaink showed a deft touch and an impressive feint in the 17th minute to see off marker Warren but Inverness keeper Dean Brill was equal to his curling left-foot shot.
Six minutes later, Hasselbaink was a threat as he found space on the left flank after being found by Stevie May's perceptive pass, but the Dutchman again could not find a way past Brill from a tight angle.
Saints obviously needed an injection of something different for the second-half and manager Tommy Wright introduced striker Chris Iwelumo in place of sitting midfielder Paddy Cregg in search of some more forward impetus.
The former Scotland international looked to have been presented with an opportunity 20 minutes into the half but he elected to lay the ball back to May instead of shooting and Warren got in a block.
The clearest sight of goal Saints got in the second half was after 57 minutes when Brill beat away David Wotherspoon's powerful shot but Hasselbaink, standing just six yards out, could not direct his header on target from the rebound.
It was symptomatic of a St Johnstone performance that lacked a cutting edge throughout, with May strangely subdued in the week he was ignored by Scotland manager Gordon Strachan for next month's friendly against Poland.
The victory will come as a huge boost for Inverness, who will be eager to maintain form ahead of their League Cup final against Aberdeen on March 16.