With consecutive wins, Kerala now have 14 points from 12 matches.
The result also meant Khalid Jamil is still unbeaten in the competition and extended NorthEast's winning run to ten games.
Goa slipped to fourth and have eight points.
Valskis scored in the 30th and 66th minute while Roy Krishna pulled one back for ATKMB in the 80th minute.
After three losses on the trot, laggards SCEB finally opened their account
This was the first time that ATK drew their first away match in an ISL match, having won in the earlier three occasions.
The goalless stalemate in the fourth edition of Indian Super League (ISL) continued for a second successive day as debutant Jamshedpur FC held NorthEast United FC to a 0-0 draw in Guwahati on Saturday.
Chennaiyin FC bounced back from a losing start in Indian Super League season 4 as they beat North East United FC 3-0 at the Jawaharlal Nehru Stadium in Chennai on Thursday.
Goian's 83rd-minute strike was enough for Chennaiyin to win the contest 1-0 and complete the ISL play-off lineup.
FC Goa clinched their first win of the ongoing Indian Super League season as they beat Kerala Blasters 3-1 at the Fatorda Stadium, in Margao, on Sunday.
Former champions ATK suffered a 0-2 defeat to two-time runners-up Kerala Blasters in the opening match of the fifth Indian Super League (ISL) at the Saltlake Stadium, in Kolkata, on Saturday.
Anwar Ali, his current side East Bengal, and parent club Delhi FC on Thursday moved the Delhi High Court and sought a stay on the suspension imposed on the player.
Jeje Lalpheklua scored two goals, including the winner in the 90th minute, as Chennaiyin FC beat ATK 3-2 in an exciting Indian Super League (ISL) match at the Jawaharlal Nehru Stadium in Chennai on Thursday.
Odisha FC were a little too predictable and Hyderabad's defenders were able to deal with them without too much discomfort.
Jamshedpur dominated proceedings and kept Kamaljit on his toes.
But the hosts did have their equaliser in the 54th minute from another corner. Rene Mihelic whipped one into the far post where Rana Gharami managed to head it back across the box. Kotal, this time around, directed it home from close-range.
Virat Kohli couldn't control his emotions when his football team crashed out of the Indian Super League (ISL) on Tuesday.
A 56th-minute penalty strike from Sunil Chhetri was the difference between the two teams
India can break into the top-50 in the FIFA rankings in the next 10 years, Sports Minister Mansukh Mandaviya said.
NorthEast United rallied to play out a thrilling 1-1 draw with Delhi Dynamos, playing their first home match of the season, to remain on top of the table in the Indian Super League football, in New Delhi, on Saturday.
Bengaluru FC and fourth-placed FC Pune City played out a listless goalless draw in the first leg semi-final of the Indian Super League match
Kerala were jolted right at the beginning when central defender Gianni Zuiverloon picked up an injury.
An unmarked Pritam Kotal got in between the Goa centre-backs and nodded the ball into the net to give them the lead.
Just as BFC looked set for a win, Machado (78th) struck again to ensure his team got a point.
Sunil Chhetri played like a man possessed as his superb hat-trick ensured a convincing 3-1 win for Bengaluru FC against FC Pune City in an entertaining second leg semi-final of this year's Indian Super League.
There was some drama at the end as ATK forced a series of corners but a goal did not materialise.
Defensive mistakes cost Bengaluru dear and helped Mumbai's cause
The Super Cup will get underway from April 3, where Kerala Blasters has been grouped together with Bengaluru FC.
Chennaiyin FC outplayed FC Goa 3-0 with a dominant performance in the second leg of the Indian Super League (ISL) semifinal to advance to the final against Bengaluru FC on 4-1 aggregate, in Chennai, on Tuesday.
Raphael Messi Bouli struck twice in the last 15 minutes to eke out a 2-2 draw for Kerala Blasters
Mumbai upped the ante and started creating a few chances after going behind.
ATK earn a dramatic 1-0 win over NorthEast United FC and reclaim the top spot
ATK produced a solid defensive display to hold an in-form Jamshedpur FC to a 1-1 draw in a Hero Indian Super League match, in Jamshedpur, on Sunday.
The club also said that an official complaint has been lodged with the appropriate authorities urging them to conduct a thorough investigation into the incident.
BFC's Augusto, Chhetri and Udanta combined in the final third but neither of the trio could apply the finishing touch.
News of all that's transpired on and off the football field
Marquez had only two training sessions with the team before naming a 26-member squad featuring new and returning players as India adapts to life after Sunil Chhetri's retirement.
Chennaiyin FC went through to the final 6-5 on aggregate, thanks to their 4-1 victory at home in the first leg.
Striker Ferran Corominas scored the first hat-trick of the season as FC Goa beat 10-man Bengaluru FC 4-3 in a thrilling match of the Indian Super League in Margao on Thursday.
Former Manchester United star and Indian Super League side ATK's coach Teddy Sheringham said it was unusual to finish a football game post midnight, something that he had never experienced in his long association with the game.
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