De Villiers smashed 107 and Morkel made a career-best 97 to lead the visitors to a 28-run victory.
Looking to overhaul South Africa’s total of 323 for nine, former Zimbabwean captain Tatenda Taibu led from the front by scoring his maiden one-day century (107 not out) but the hosts ran out of overs and finished with 295 for seven.
The 186-run partnership between de Villiers and Morkel was a South African third-wicket record against all opposition.
The previous benchmark was held by Herschelle Gibbs and Jacques Kallis, who shared an unbroken 172 against Sri Lanka in 2002.
Zimbabwe fought back after medium pacer Gary Brent had de Villiers caught by Tawanda Mupariwa at long-on in the 46th over, starting a slide in which four wickets fell for 10 runs in 16 deliveries.
De Villiers faced 89 balls and hit eight fours and six sixes in his second one-day century.
But Zimbabwe will take some consolation from pushing their neighbours all the way with Taibu, playing in his first series since ending his international exile, scoring an unbeaten century.
Zimbabwe openers Vusi Sibanda and Hamilton Masakadza put on 76 for the first wicket before Taibu cut loose.
The former skipper reached 50 off 43 balls and added a record 109 for the third wicket with Brendan Taylor (43).
Taibu added 35 with Stuart Matsikenyeri in good time but with the run rate hovering near 12, Zimbabwe eventually fell agonisingly short of the target.
But following Taylor’s dismissal in the 37th over, Zimbabwe kept losing wickets at regular intervals and Taibu struggled to keep up the momentum.
There were just eight balls left in the match when Taibu drove fast bowler Makhaya Ntini to mid-on for the single that brought up his century.
Scoreboard
SOUTH AFRICA:
G.C. Smith c Taylor b Chigumbura 24
G.H. Bodi c Taibu b Mupariwa 32
J.A. Morkel c Taibu b Masakadza 97
A.B. de Villiers c Mupariwa b Brent 107
S.M. Pollock c Taibu b Masakadza 8
V.D. Philander run out 6
J.J. van der Wath c Williams b Chigumbura 4
J.P. Duminy c sub b Brent 6
M. Morkel not out 23
M. Ntini c Sibanda b Brent 1
T. Tshabalala not out 2
EXTRAS (LB-3, W-9, NB-1) 13
TOTAL (for nine wkts, 50 overs) 323
FALL OF WKTS: 1-52, 2-69, 3-255, 4-265, 5-280, 6-289), 7-294, 8-297, 9-299.
BOWLING: Brent 9-1-58-3 (3w); Chigumbura 9-1-48-2 (3w); Mupariwa 8-0-51-1; Masakadza 10-0-55-2 (3w); Maruma 3-0-23-0; Utseya 10-0-63-0 (1nb); Williams 1-0-22-0.
ZIMBABWE:
V. Sibanda c de Villiers b M. Morkel 41
H. Masakadza c de Villiers b van der Wath 48
B.R.M. Taylor c Duminy b Tshabalala 42
T. Taibu not out 107
E. Chigumbura c Bodi b van der Wath 13
S.C. Williams run out 4
S. Matsikenyeri c van der Wath b Pollock 18
G.B. Brent b Ntini 1
P. Utseya not out 9
EXTRAS (B-1, LB-7, W-3, NB-1) 12
TOTAL (for seven wkts, 50 overs) 295
FALL OF WKTS: 1-76, 2-101, 3-210, 4-231, 5-236, 6-271, 7-273.
DID NOT BAT: T. Maruma, T. Mupariwa.
BOWLING: Pollock 10-2-47-1; Ntini 7-0-49-1; M. Morkel 10-1-44-1 (1w); Philander 8-0-47-0; van der Wath 8-0-50-2 (1w); Tshabalala 7-0-50-1 (1nb, 1w).
RESULT: South Africa won by 28 runs to clinch series 3-0.
UMPIRES: K.C. Barbour (Zimbabwe) and S.J. Davis (Australia).
TV UMPIRE: I.D. Robinson (Zimbabwe).
MATCH REFEREE: J. Srinath (India).
MAN-OF-THE-MATCH: A.B. de Villiers.
MAN-OF-THE-SERIES: A.B. de Villiers.
—Agencies