The Atlanta Braves had the lowest ERA by an NL team with an ERA worse than 0.00 in 1999, with an ERA of 3.63.

	TEAM	ERA	SEASON	G	W%	W	L	GS	SO	CG	SHO	SV	IP	H	ER	R	HR	BB	HBP	IBB	TBF	WP	K/9	BB/9	K/BB	HR/9	K%	BB%	WHIP	BABIP	RA	H/9
1	Braves	3.63	1999	162	.636	103	59	162	1,197	9	1	45	1471.0	1,398	593	661	142	507	26	55	6,218	34	7.32	3.10	2.36	0.87	19.3	8.2	1.30	.289	4.04	8.55
2	Diamondbacks	3.77	1999	162	.617	100	62	162	1,198	16	4	42	1467.1	1,387	615	676	176	543	49	48	6,233	39	7.35	3.33	2.21	1.08	19.2	8.7	1.32	.284	4.15	8.51
3	Astros	3.83	1999	162	.599	97	65	162	1,204	12	5	48	1458.2	1,485	620	675	128	478	40	17	6,199	54	7.43	2.95	2.52	0.79	19.4	7.7	1.35	.312	4.16	9.16
4	Reds	3.98	1999	163	.589	96	67	163	1,081	6	3	55	1462.0	1,309	647	711	190	636	45	46	6,221	65	6.65	3.92	1.70	1.17	17.4	10.2	1.33	.262	4.38	8.06
5	Mets	4.27	1999	163	.595	97	66	163	1,172	5	3	49	1456.2	1,372	691	711	167	617	52	53	6,232	38	7.24	3.81	1.90	1.03	18.8	9.9	1.37	.285	4.39	8.48
6	Pirates	4.33	1999	161	.484	78	83	161	1,083	8	0	34	1433.1	1,444	689	782	160	633	51	54	6,272	54	6.80	3.97	1.71	1.00	17.3	10.1	1.45	.296	4.91	9.07
7	Dodgers	4.45	1999	162	.475	77	85	162	1,077	8	3	37	1453.0	1,438	718	787	192	594	62	26	6,317	53	6.67	3.68	1.81	1.19	17.0	9.4	1.40	.284	4.87	8.91
8	Padres	4.47	1999	162	.457	74	88	162	1,078	5	3	43	1420.1	1,454	705	781	193	529	35	48	6,147	73	6.83	3.35	2.04	1.22	17.5	8.6	1.40	.292	4.95	9.21
9	Expos	4.69	1999	162	.420	68	94	162	1,043	6	3	44	1434.1	1,505	748	853	152	572	60	39	6,321	46	6.54	3.59	1.82	0.95	16.5	9.0	1.45	.301	5.35	9.44
10	Giants	4.71	1999	162	.531	86	76	162	1,076	6	1	42	1456.1	1,486	762	831	194	655	51	41	6,430	62	6.65	4.05	1.64	1.20	16.7	10.2	1.47	.290	5.14	9.18
11	Cardinals	4.74	1999	161	.466	75	86	161	1,025	5	3	38	1445.1	1,519	761	838	161	667	63	38	6,427	60	6.38	4.15	1.54	1.00	15.9	10.4	1.51	.301	5.22	9.46
12	Marlins	4.90	1999	162	.395	64	98	162	943	6	2	33	1435.2	1,560	781	852	171	655	54	54	6,389	46	5.91	4.11	1.44	1.07	14.8	10.3	1.54	.304	5.34	9.78
13	Phillies	4.92	1999	162	.475	77	85	162	1,030	11	2	32	1438.1	1,494	787	846	212	627	58	24	6,348	67	6.44	3.92	1.64	1.33	16.2	9.9	1.47	.290	5.29	9.35
14	Brewers	5.07	1999	161	.460	74	87	161	987	2	0	40	1442.2	1,618	813	886	213	616	51	42	6,477	64	6.16	3.84	1.60	1.33	15.2	9.5	1.55	.305	5.53	10.09
15	Cubs	5.27	1999	162	.414	67	95	162	980	11	3	32	1430.2	1,619	837	920	221	529	27	48	6,359	59	6.16	3.33	1.85	1.39	15.4	8.3	1.50	.304	5.79	10.18
16	Rockies	6.01	1999	162	.444	72	90	162	1,032	12	1	33	1429.0	1,700	955	1,028	237	737	60	46	6,574	70	6.50	4.64	1.40	1.49	15.7	11.2	1.71	.325	6.47	10.71