It was not pretty but the victory kept the Cape franchise in second spot on the overall competition log, where the Stormers needed a bonus point victory from four tries to pass top positioned Chiefs on the table.
Attractive running rugby in some heavy rain was never an option, though, the Cheetahs were always in the game but for some poor decision-making and lapses in concentration on their defence.
The hosts kicked away too much possession in first half that gave hard earned possession back to the Stormers.
In inclement weather, a kicking approach was always the first option, but the Cheetahs didn't put any pressure on the Stormers.
In turn, they kicked well tactically with the visitors' scrumhalf Dewaldt Duvenhage pinning them down to their own half.
The Stormers are known for their prowess in the wet, but their line outs were in a shambles early on as they twice conceded possession because the throw went astray.
Their attacking play was up to scratch, however, and kept piling on the pressure before finally getting on the board first after flyhalf Peter Grant kicked a penalty in the 17th minute.
They might not have been at their best on the attack, but the Cheetahs were better than the Stormers in the scrums — even though the visitors were 20 kilograms heavier.
The hosts front row of Trevor Nyakane, Adriaan Strauss and WP Nel had the Capetonians under immense pressure in the first stanza.
The Stormers started the second half at high pace, applying pressure with some positive attacking play.
Kept their cool
The hosts struggled to absorb the pressure with fullback Willie le Roux sin binned after some deliberate offside play.
The line kick put the visitors five metres from the Cheetahs goal line, but even with one man short, the Cheetahs defence held on.
Grant went on to kick his second penalty after the hosts infringed at the breakdown.
The Cheetahs themselves looked much better on the attack than in the first stanza, and started tackling the visitors back and forcing penalties at the breakdown.
At one such instance, Smit kicked his second penalty to draw the scores level again, but the home team's happiness was short lived.
From the resulting kick off, Grant put in a kick behind the Cheetahs and the ball bounced right for winger Gio Aplon to jog over.
The Cheetahs had the best of the possession in the last 15 minutes, but the Stormers proved once again why their defence is considered the best in the competition as they kept their cool to hold on to the win.
Stormers 13 (3): Tries: Gio Aplon. Conversions: Peter Grant. Penalties: Peter Grant (2).
Cheetahs 6 (3): Penalties: Riaan Smit (2). — Sapa.