Coutinho is a great player who has given us a lot and will give us a lot.
However, the big names are set to return at the Camp Nou on Sunday as Barca aim to extend their lead at the top of the La Liga table.
"He should be proud", said Suarez, who scored Barcelona's other two goals.
In fact, this was one of Messi's quieter nights in terms of performance and in another team it might have been Suarez or Philippe Coutinho picking up the plaudits.
The fact that they scored in three of those encounters may be a minor source of encouragement but their tally of five away goals this season is the lowest in the division.
Ballon d'Or victor Luka Modric opened the scoring for Madrid with a left-footed effort after 13 minutes. Arthur Melo started it, playing a one-two with Coutinho and then into the feet of Sergio Busquets.
Luis Suarez opened the scoring, before Messi made it 2-0.
Messi's milestone strike came moments after he appeared to be struggling.
Coutinho signed for Barca in January past year and was cup-tied in the Champions League, but he impressed in the second half of the campaign at Camp Nou, scoring 10 goals in 22 appearances as Barca won LaLiga and the Copa del Rey.
The next most prolific scorer in LaLiga history, Cristiano Ronaldo, has 311 in the competition but will not be bothering Messi's record after his move last summer from Real Madrid to Juventus.
Luka Modric sent a thunderous shot into the top corner but Betis looked to be in the ascendancy after Sergio Canales poked in a second-half equaliser.
Catalunya Radio have reported that club representative Andre Cury - who played a key role in Barca's signing of Neymar from Santos in 2013 - has met with Neymar and his team as interest around a potential return for a player who left in 2017 gathers pace.
Third-placed Sevilla lost 2-0 at Athletic Bilbao, ending its unbeaten run in nine rounds.
That being said, let Coutinho leave would be a massive mistake.